#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
HYDIN	54768	hgsc.bcm.edu	37	16	70934989	70934989	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:70934989delA	ENST00000393567.2	-	53	9116	c.8966delT	c.(8965-8967)atcfs	p.I2989fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2989					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CTCAGGGGGGATGGTCCCCTG	0.572																																					p.I2989fs		Atlas-Indel	.											.	HYDIN	788	.	0			c.8967delC						PASS	.						164.0	157.0	159.0					16																	70934989		2024	4189	6213	SO:0001589	frameshift_variant	54768	exon53			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8966delT	16.37:g.70934989delA	ENSP00000377197:p.Ile2989fs	45.0	0.0	0		110.0	16.0	0.145455	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	none		0.572	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
OR6A2	8590	hgsc.bcm.edu	37	11	6816750	6816751	+	Frame_Shift_Ins	INS	-	-	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6816750_6816751insA	ENST00000332601.3	-	1	377_378	c.189_190insT	c.(187-192)tttctafs	p.L64fs		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	64					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|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)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATATTAGCTAGAAAAAAGTACA	0.441																																					p.L64fs		Atlas-Indel	.											.	OR6A2	68	.	0			c.190_191insT						PASS	.																																			SO:0001589	frameshift_variant	8590	exon1			.	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.190dupT	11.37:g.6816756_6816756dupA	ENSP00000330384:p.Leu64fs	149.0	0.0	0		157.0	33.0	0.210191	NM_003696	Q3MJC7|Q6IF35|Q9H206	Frame_Shift_Ins	INS	ENST00000332601.3	37	CCDS7772.1																																																																																			.	.	none		0.441	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696	
FAM115C	285966	hgsc.bcm.edu	37	7	143417404	143417405	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143417404_143417405delCT	ENST00000441159.2	+	3	1318_1319	c.1252_1253delCT	c.(1252-1254)ctcfs	p.L418fs	FAM115C_ENST00000411497.2_Frame_Shift_Del_p.L137fs|FAM115C_ENST00000444908.2_Frame_Shift_Del_p.L418fs|FAM115C_ENST00000409703.3_Frame_Shift_Del_p.L254fs|FAM115C_ENST00000411935.1_Frame_Shift_Del_p.L254fs|FAM115C_ENST00000425618.2_Frame_Shift_Del_p.L137fs|FAM115C_ENST00000357344.4_Frame_Shift_Del_p.L418fs			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	418					hematopoietic progenitor cell differentiation (GO:0002244)					endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						CCGCAAGGCGCTCTCTCAATTC	0.53																																					p.417_418del		Atlas-Indel	.											.	FAM115C	29	.	0			c.1251_1252del						PASS	.		,,	39,207		18,3,102					,,	-7.1	0.0			1	22,442		10,2,220	no	frameshift,frameshift,frameshift	FAM115C	NM_173678.2,NM_001130026.2,NM_001130025.1	,,	28,5,322	A1A1,A1R,RR		4.7414,15.8537,8.5915	,,	,,		61,649				SO:0001589	frameshift_variant	285966	exon3			.	AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"""family with sequence similarity 139, member A"""	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.1252_1253delCT	7.37:g.143417408_143417409delCT	ENSP00000404265:p.Leu418fs	106.0	0.0	0		87.0	16.0	0.183908	NM_173678	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Frame_Shift_Del	DEL	ENST00000441159.2	37																																																																																				.	.	none		0.530	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330287.1	NM_173678	
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	rs148187838|rs566862006	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170387132_170387133insT	ENST00000453153.2	-	14	2752_2753	c.2406_2407insA	c.(2404-2409)aaacgafs	p.R803fs	FASTKD1_ENST00000453929.2_Frame_Shift_Ins_p.R760fs|FASTKD1_ENST00000495505.1_5'UTR	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	803	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						TCCAAATGTCGTTTTTTCATAG	0.342													TTTTTT|TTTTTT|TTTTTTT|insertion	18	0.00359425	0.0008	0.0029	5008	,	,		15503	0.0		0.007	False		,,,				2504	0.0082				p.R803fs		Pindel,Atlas-Indel	.											.	FASTKD1	86	.	0			c.2407_2408insA						PASS	.			8,4258		0,8,2125						3.3	1.0			159	99,8155		1,97,4029	no	frameshift	FASTKD1	NM_024622.3		1,105,6154	A1A1,A1R,RR		1.1994,0.1875,0.8546				107,12413				SO:0001589	frameshift_variant	79675	exon14			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.2407dupA	2.37:g.170387138_170387138dupT	ENSP00000400513:p.Arg803fs	190.0	0.0	.		222.0	69.0	0.311	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Ins	INS	ENST00000453153.2	37	CCDS33318.1																																																																																			.	.	none		0.342	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
FARP2	9855	hgsc.bcm.edu	37	2	242407679	242407680	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242407679_242407680delCT	ENST00000264042.3	+	18	2188_2189	c.2018_2019delCT	c.(2017-2019)cctfs	p.P673fs		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	673	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		TGCTACTTGCCTCTCAACACGT	0.564																																					p.673_673del		Pindel,Atlas-Indel	.											.	FARP2	92	.	0			c.2017_2018del						PASS	.			18,4248		9,0,2124						5.0	1.0			109	40,8212		19,2,4105	no	frameshift	FARP2	NM_014808.2		28,2,6229	A1A1,A1R,RR		0.4847,0.4219,0.4633				58,12460				SO:0001589	frameshift_variant	9855	exon18			.	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.2018_2019delCT	2.37:g.242407681_242407682delCT	ENSP00000264042:p.Pro673fs	82.0	0.0	.		62.0	17.0	0.274	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	37	CCDS33424.1																																																																																			.	.	none		0.564	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
NCL	4691	hgsc.bcm.edu	37	2	232325406	232325408	+	In_Frame_Del	DEL	TCA	TCA	-	rs556842200|rs200406507	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:232325406_232325408delTCA	ENST00000322723.4	-	4	1023_1025	c.783_785delTGA	c.(781-786)gatgag>gag	p.D261del	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	261	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TTCCTCCTCCtcatcatcttcat	0.433														27	0.00539137	0.0023	0.0043	5008	,	,		27425	0.006		0.004	False		,,,				2504	0.0112				p.262_262del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.784_786del						PASS	.			103,4161		0,103,2029						-8.8	0.0		dbSNP_130	203	81,8169		0,81,4044	no	coding	NCL	NM_005381.2		0,184,6073	A1A1,A1R,RR		0.9818,2.4156,1.4704				184,12330				SO:0001651	inframe_deletion	4691	exon4			.		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.783_785delTGA	2.37:g.232325409_232325411delTCA	ENSP00000318195:p.Asp261del	154.0	0.0	.		153.0	34.0	0.222	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	none		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
TET2	54790	hgsc.bcm.edu	37	4	106158509	106158510	+	Splice_Site	INS	-	-	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106158509_106158510insT	ENST00000540549.1	+	3	4269		c.e3+1		TET2_ENST00000380013.4_Splice_Site|TET2_ENST00000305737.2_Frame_Shift_Ins_p.K1138fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.K1138fs|TET2_ENST00000513237.1_Splice_Site|TET2_ENST00000413648.2_Splice_Site|TET2_ENST00000545826.1_Splice_Site			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2						5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		AGATGTGTAGGTAAGTGCCAGA	0.342			"""Mis N, F"""		MDS																																p.G1137fs		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.3410_3411insT						PASS	.																																			SO:0001630	splice_region_variant	54790	exon3			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.3409+1->T	4.37:g.106158510_106158510dupT		250.0	0.0	.		272.0	55.0	0.202	NM_017628	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.342	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	Intron
MUC4	4585	hgsc.bcm.edu	37	3	195505765	195505766	+	Frame_Shift_Ins	INS	-	-	A	rs570547323|rs558507786	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505765_195505766insA	ENST00000463781.3	-	2	13144_13145	c.12685_12686insT	c.(12685-12687)agcfs	p.S4229fs	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Frame_Shift_Ins_p.S4229fs|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	986					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAAGGCTGGTGACAGGA	0.579																																					p.S4229fs		Atlas-Indel	.											.	MUC4	1505	.	0			c.12686_12687insT						PASS	.																																			SO:0001589	frameshift_variant	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12685_12686insT	3.37:g.195505765_195505766insA	ENSP00000417498:p.Ser4229fs	91.0	0.0	0		68.0	10.0	0.147059	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Frame_Shift_Ins	INS	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.579	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF660	285349	hgsc.bcm.edu	37	3	44636279	44636280	+	Frame_Shift_Del	DEL	AT	AT	-	rs552732245	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44636279_44636280delAT	ENST00000322734.2	+	3	927_928	c.594_595delAT	c.(592-597)acatgtfs	p.C199fs	RP11-944L7.4_ENST00000457331.1_RNA	NM_173658.2	NP_775929.2	Q6AZW8	ZN660_HUMAN	zinc finger protein 660	199					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		GTGGGAAAACATGTGGTTCTAA	0.386														5	0.000998403	0.0	0.0	5008	,	,		21714	0.0		0.005	False		,,,				2504	0.0				p.198_198del		Pindel,Atlas-Indel	.											.	ZNF660	28	.	0			c.593_594del						PASS	.			4,4262		0,4,2129						4.3	1.0			87	60,8192		0,60,4066	no	frameshift	ZNF660	NM_173658.2		0,64,6195	A1A1,A1R,RR		0.7271,0.0938,0.5113				64,12454				SO:0001589	frameshift_variant	285349	exon3			.	AK094189	CCDS2716.1	3p21.32	2013-01-08			ENSG00000144792	ENSG00000144792		"""Zinc fingers, C2H2-type"""	26720	protein-coding gene	gene with protein product							Standard	NM_173658		Approved	FLJ36870	uc003cnl.1	Q6AZW8	OTTHUMG00000133097	ENST00000322734.2:c.594_595delAT	3.37:g.44636279_44636280delAT	ENSP00000324605:p.Cys199fs	41.0	0.0	.		38.0	13.0	0.342	NM_173658	Q7Z331|Q8N9M8	Frame_Shift_Del	DEL	ENST00000322734.2	37	CCDS2716.1																																																																																			.	.	none		0.386	ZNF660-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256756.4	NM_173658	
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487252	18487253	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18487252_18487253delAC	ENST00000280706.2	+	3	1110_1111	c.313_314delAC	c.(313-315)acafs	p.T105fs	LDHAL6A_ENST00000396213.3_Frame_Shift_Del_p.T105fs	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	105					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						AAAAGGAGAAACACGCCTTGAT	0.376																																					p.104_105del		Pindel,Atlas-Indel	.											.	LDHAL6A	35	.	0			c.312_313del						PASS	.																																			SO:0001589	frameshift_variant	160287	exon3			.	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.313_314delAC	11.37:g.18487254_18487255delAC	ENSP00000280706:p.Thr105fs	152.0	0.0	.		179.0	56.0	0.313	NM_144972	D3DQY5	Frame_Shift_Del	DEL	ENST00000280706.2	37	CCDS7841.1																																																																																			.	.	none		0.376	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329897	24329908	+	IGR	DEL	AGCAGGAGCAGG	AGCAGGAGCAGG	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCAGGAGCAGG	AGCAGGAGCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:24329897_24329908delAGCAGGAGCAGG								AC096509.1 (25103 upstream) : AC004552.1 (37017 downstream)																							caggagcagcagcaggagcaggagcaggagca	0.604																																					p.509_513del		Atlas-Indel	.											.	.	.	.	0			c.1526_1537del						PASS	.																																			SO:0001628	intergenic_variant	170067	exon1			.																													X.37:g.24329897_24329908delAGCAGGAGCAGG		101.0	0.0	0		153.0	38.0	0.248366	NM_001136233		In_Frame_Del	DEL		37																																																																																				.	.	none	0	0.604								
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG	rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39305774_39305775insTGGCAGCAGCTGGGG	ENST00000343246.4	-	1	279_280	c.245_246insCCCCAGCTGCTGCCA	c.(244-246)cag>caCCCCAGCTGCTGCCAg	p.81_82insHPSCC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	81	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.Q82H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcaggtggtctggcagcagca	0.653																																					p.Q82delinsHPSCCQ		Atlas-Indel	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	1	Substitution - Missense(1)	lung(1)	c.246_247insCCCCAGCTGCTGCCA						PASS	.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.245_246insCCCCAGCTGCTGCCA	17.37:g.39305774_39305775insTGGCAGCAGCTGGGG	ENSP00000340546:p.Cys81_Gln82insHisProSerCysCys	22.0	0.0	0		31.0	17.0	0.548387	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
HYDIN	54768	hgsc.bcm.edu	37	16	70934990	70934991	+	In_Frame_Ins	INS	-	-	CCC			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:70934990_70934991insCCC	ENST00000393567.2	-	53	9114_9115	c.8964_8965insGGG	c.(8962-8967)accatc>accGGGatc	p.2988_2989TI>TGI		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2988					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCAGGGGGGATGGTCCCCTGCA	0.564																																					p.I2989delinsGI		Atlas-Indel	.											.	HYDIN	788	.	0			c.8965_8966insGGG						PASS	.																																			SO:0001652	inframe_insertion	54768	exon53			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.8964_8965insGGG	16.37:g.70934990_70934991insCCC	ENSP00000377197:p.Thr2988_Ile2989insGly	47.0	0.0	0		108.0	16.0	0.148148	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	In_Frame_Ins	INS	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	none		0.564	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784008	+	Splice_Site	DEL	TATA	TATA	-	rs577313725|rs548723883|rs75318507|rs201697727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATA	TATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39784005_39784008delTATA	ENST00000280083.3	+	15	1670		c.e15+2		CTAGE5_ENST00000396158.2_Splice_Site|RP11-407N17.3_ENST00000553728.1_Splice_Site|CTAGE5_ENST00000341502.5_Splice_Site|CTAGE5_ENST00000341749.3_Splice_Site|CTAGE5_ENST00000396165.4_Splice_Site|CTAGE5_ENST00000553352.1_Splice_Site|CTAGE5_ENST00000557038.1_Splice_Site|CTAGE5_ENST00000556148.1_Splice_Site|RP11-407N17.3_ENST00000603904.1_Splice_Site|CTAGE5_ENST00000348007.3_Splice_Site			O15320	CTGE5_HUMAN	CTAGE family, member 5						positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.?(1)	CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		CAAGGGCAGGTATATATATAtgtg	0.299														6	0.00119808	0.0	0.0043	5008	,	,		13080	0.001		0.002	False		,,,				2504	0.0				.		Atlas-Indel	.											.	CTAGE5	75	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	.						PASS	.																																			SO:0001630	splice_region_variant	4253	.			.	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1356+2TATA>-	14.37:g.39784009_39784012delTATA		116.0	0.0	0		131.0	79.0	0.603053	.	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Splice_Site	DEL	ENST00000280083.3	37	CCDS9674.1																																																																																			.	.	alt		0.299	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	Intron
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:67802190delA	ENST00000377865.2	-	1	517	c.383delT	c.(382-384)atafs	p.I128fs	PCDH9_ENST00000328454.5_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000456367.1_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000544246.1_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000377861.3_Frame_Shift_Del_p.I128fs			Q9HC56	PCDH9_HUMAN	protocadherin 9	128	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AATTATTTTTATTTTGATCAG	0.408																																					p.I128fs		Atlas-Indel	.											.	PCDH9	252	.	0			c.384delA						PASS	.						87.0	89.0	88.0					13																	67802190		2203	4300	6503	SO:0001589	frameshift_variant	5101	exon2			.	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.383delT	13.37:g.67802190delA	ENSP00000367096:p.Ile128fs	103.0	0.0	0		154.0	12.0	0.0779221	NM_020403	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Frame_Shift_Del	DEL	ENST00000377865.2	37	CCDS9444.1																																																																																			.	.	none		0.408	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382374	24382388	+	IGR	DEL	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	-	rs371342199		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:24382374_24382388delTGCTGCTGCTGCTGC								AC004552.1 (15351 upstream) : PDK3 (100949 downstream)																							ctgctgctattgctgctgctgctgctgctgctgct	0.577																																					p.499_504del		Atlas-Indel	.											.	.	.	.	0			c.1496_1510del						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382374_24382388delTGCTGCTGCTGCTGC		131.0	0.0	0		195.0	52.0	0.266667	NM_001136234		In_Frame_Del	DEL		37																																																																																				.	.	alt	0	0.577								
MROH2B	133558	hgsc.bcm.edu	37	5	41064591	41064598	+	Frame_Shift_Del	DEL	TTCATCCT	TTCATCCT	-	rs377494374|rs533532784		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTCATCCT	TTCATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:41064591_41064598delTTCATCCT	ENST00000399564.4	-	5	886_893	c.436_443delAGGATGAA	c.(436-444)aggatgaagfs	p.RMK146fs		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	146																	GAAAGTCCCCTTCATCCTTTCATCCTCG	0.462																																					p.146_148del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.437_444del						PASS	.			32,3684		15,2,1841						0.8	0.6			86	127,7795		50,27,3884	no	frameshift	HEATR7B2	NM_173489.4		65,29,5725	A1A1,A1R,RR		1.6031,0.8611,1.3662				159,11479				SO:0001589	frameshift_variant	133558	exon5			.		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.436_443delAGGATGAA	5.37:g.41064599_41064606delTTCATCCT	ENSP00000382476:p.Arg146fs	46.0	0.0	.		36.0	13.0	0.361	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Frame_Shift_Del	DEL	ENST00000399564.4	37	CCDS47202.1																																																																																			.	.	none		0.462	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
UHRF2	115426	hgsc.bcm.edu	37	9	6413513	6413513	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413513delT	ENST00000276893.5	+	1	191	c.23delT	c.(22-24)attfs	p.I8fs	UHRF2_ENST00000381373.3_Frame_Shift_Del_p.I8fs|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	8	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		GTTCGCACCATTGATGGCTCC	0.667																																					p.I8fs		Atlas-Indel	.											.	UHRF2	50	.	0			c.22delA						PASS	.						60.0	60.0	60.0					9																	6413513		2203	4300	6503	SO:0001589	frameshift_variant	115426	exon1			.	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.23delT	9.37:g.6413513delT	ENSP00000276893:p.Ile8fs	87.0	0.0	0		75.0	14.0	0.186667	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Frame_Shift_Del	DEL	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.667	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
TSR1	55720	hgsc.bcm.edu	37	17	2237939	2237941	+	In_Frame_Del	DEL	CCA	CCA	-	rs570684854	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2237939_2237941delCCA	ENST00000301364.5	-	5	1885_1887	c.806_808delTGG	c.(805-810)gtgggc>ggc	p.V269del	SGSM2_ENST00000268989.3_5'Flank|SGSM2_ENST00000574563.1_5'Flank|TSR1_ENST00000576112.2_In_Frame_Del_p.V253del|SGSM2_ENST00000426855.2_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	269					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TTCAAGGTGCCCACCAAGTTATT	0.443														7	0.00139776	0.0	0.0029	5008	,	,		18232	0.0		0.005	False		,,,				2504	0.0				p.269_270del		Pindel,Atlas-Indel	.											.	TSR1	57	.	0			c.807_809del						PASS	.			4,4252		0,4,2124						5.4	1.0			110	47,8205		2,43,4081	no	coding	TSR1	NM_018128.4		2,47,6205	A1A1,A1R,RR		0.5696,0.094,0.4077				51,12457				SO:0001651	inframe_deletion	55720	exon5			.	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.806_808delTGG	17.37:g.2237942_2237944delCCA	ENSP00000301364:p.Val269del	110.0	0.0	.		87.0	29.0	0.333	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	In_Frame_Del	DEL	ENST00000301364.5	37	CCDS32525.1																																																																																			.	.	none		0.443	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
GCC2	9648	hgsc.bcm.edu	37	2	109087929	109087931	+	In_Frame_Del	DEL	AAG	AAG	-	rs553103180		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:109087929_109087931delAAG	ENST00000309863.6	+	6	2858_2860	c.2144_2146delAAG	c.(2143-2148)aaagaa>aaa	p.E716del		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	716					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						TTGTCTCAAAAAGAAGATGTTAT	0.305																																					p.715_715del		Pindel,Atlas-Indel	.											.	GCC2	129	.	0			c.2143_2145del						PASS	.			4,4246		1,2,2122						4.2	1.0			133	12,8222		2,8,4107	no	coding	GCC2	NM_181453.3		3,10,6229	A1A1,A1R,RR		0.1457,0.0941,0.1282				16,12468				SO:0001651	inframe_deletion	9648	exon6			.	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2144_2146delAAG	2.37:g.109087932_109087934delAAG	ENSP00000307939:p.Glu716del	109.0	0.0	.		83.0	24.0	0.289	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	In_Frame_Del	DEL	ENST00000309863.6	37	CCDS33268.1																																																																																			.	.	none		0.305	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
TET2	54790	hgsc.bcm.edu	37	4	106196525	106196525	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106196525delG	ENST00000540549.1	+	11	5718	c.4858delG	c.(4858-4860)gggfs	p.G1620fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.G1620fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.G1641fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1620					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CCCTTACCCTGGGCTTTTGAA	0.433			"""Mis N, F"""		MDS																																p.P1619fs		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.4857delT						PASS	.						47.0	40.0	42.0					4																	106196525		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4858delG	4.37:g.106196525delG	ENSP00000442788:p.Gly1620fs	96.0	0.0	.		76.0	13.0	0.171	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.433	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	rs534542684	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:58899157delG	ENST00000556134.1	+	5	621	c.347delG	c.(346-348)agafs	p.R116fs	KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.R143fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs|KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.R46fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	116					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GATGCTCTAAGAACAGTTTTA	0.279													G|G|-|deletion	12	0.00239617	0.0	0.0058	5008	,	,		15268	0.0		0.007	False		,,,				2504	0.001				p.R143fs		Pindel,Atlas-Indel	.											.	KIAA0586	180	.	0			c.427delA						PASS	.			3,3511		0,3,1754	44.0	43.0	43.0			5.2	1.0	14		43	25,7757		0,25,3866	no	frameshift	KIAA0586	NM_014749.3		0,28,5620	A1A1,A1R,RR		0.3213,0.0854,0.2479			58899157	28,11268	1814	4055	5869	SO:0001589	frameshift_variant	9786	exon5			.	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.347delG	14.37:g.58899157delG	ENSP00000452351:p.Arg116fs	170.0	0.0	.		152.0	56.0	0.368	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	none		0.279	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230370	23230370	+	Frame_Shift_Del	DEL	A	A	-	rs538001103	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:23230370delA	ENST00000526893.1	+	1	411	c.137delA	c.(136-138)caafs	p.Q46fs	IGLL5_ENST00000531372.1_Frame_Shift_Del_p.Q46fs|IGLL5_ENST00000532223.2_Frame_Shift_Del_p.Q46fs|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	46						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GTTGCACCGCAAAGCGGGGAC	0.682																																					p.Q46fs		Pindel,Atlas-Indel	.											.	IGLL5	26	.	0			c.136delC						PASS	.																																			SO:0001589	frameshift_variant	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.137delA	22.37:g.23230370delA	ENSP00000431254:p.Gln46fs	144.0	0.0	.		45.0	10.0	0.222	NM_001178126		Frame_Shift_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
MUC4	4585	hgsc.bcm.edu	37	3	195505762	195505763	+	Frame_Shift_Del	DEL	AG	AG	-	rs534260673|rs566782506	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505762_195505763delAG	ENST00000463781.3	-	2	13147_13148	c.12688_12689delCT	c.(12688-12690)cttfs	p.L4230fs	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Frame_Shift_Del_p.L4230fs|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	987					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L4230F(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TACTGAGGAAAGGCTGGTGACA	0.579																																					p.4230_4230del		Atlas-Indel	.											MUC4_ENST00000463781,NS,carcinoma,-2,4	MUC4	1505	4	2	Substitution - Missense(2)	kidney(2)	c.12689_12690del						PASS	.																																			SO:0001589	frameshift_variant	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12688_12689delCT	3.37:g.195505762_195505763delAG	ENSP00000417498:p.Leu4230fs	88.0	0.0	0		68.0	10.0	0.147059	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Frame_Shift_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.579	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF543	125919	hgsc.bcm.edu	37	19	57839629	57839630	+	In_Frame_Ins	INS	-	-	GCG			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57839629_57839630insGCG	ENST00000321545.4	+	4	1144_1145	c.799_800insGCG	c.(799-801)agg>aGCGgg	p.267_267R>SG		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTTTAACCGCAGGTCACACCTC	0.51																																					p.R267delinsSG		Pindel,Atlas-Indel	.											.	ZNF543	61	.	0			c.799_800insGCG						PASS	.			0,4264		0,0,2132						2.6	0.3			64	1,8253		0,1,4126	no	coding	ZNF543	NM_213598.3		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				SO:0001652	inframe_insertion	125919	exon4			.	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		Exception_encountered	19.37:g.57839629_57839630insGCG	ENSP00000322545:p.Arg267delinsSerGly	55.0	0.0	.		47.0	20.0	0.426	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	In_Frame_Ins	INS	ENST00000321545.4	37	CCDS33130.1																																																																																			.	.	none		0.510	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
DDN	23109	hgsc.bcm.edu	37	12	49391394	49391395	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49391394_49391395insC	ENST00000421952.2	-	2	1285_1286	c.1264_1265insG	c.(1264-1266)gcafs	p.A422fs	RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	422	Interaction with ACTN1.|Interaction with CD2AP and NPHS1. {ECO:0000250}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						CTCCGGTCCTGCCCCCTCTCCA	0.663																																					p.A422fs		Pindel,Atlas-Indel	.											.	DDN	54	.	0			c.1265_1266insG						PASS	.																																			SO:0001589	frameshift_variant	23109	exon2			.	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.1265dupG	12.37:g.49391399_49391399dupC	ENSP00000390590:p.Ala422fs	41.0	0.0	.		52.0	11.0	0.212	NM_015086		Frame_Shift_Ins	INS	ENST00000421952.2	37	CCDS31791.2																																																																																			.	.	none		0.663	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
ZNF623	9831	hgsc.bcm.edu	37	8	144733650	144733654	+	Stop_Codon_Del	DEL	ATAAA	ATAAA	-	rs202122969|rs376588040		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ATAAA	ATAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144733650_144733654delATAAA	ENST00000501748.2	+	0	1697_1701				ZNF623_ENST00000458270.2_Stop_Codon_Del|ZNF623_ENST00000526926.1_Stop_Codon_Del	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623						regulation of transcription, DNA-templated (GO:0006355)|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(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGGTAACTTATAAAATAATTACTT	0.415																																					p.536_537del		Pindel,Atlas-Indel	.											.	ZNF623	63	.	0			c.1607_1611del						PASS	.		,	67,4197		0,67,2065					,	-1.8	0.0			55	7,8247		0,7,4120	no	frameshift,frameshift	ZNF623	NM_014789.3,NM_001082480.1	,	0,74,6185	A1A1,A1R,RR		0.0848,1.5713,0.5911	,	,		74,12444				SO:0001567	stop_retained_variant	9831	exon1			.	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		Exception_encountered	8.37:g.144733650_144733654delATAAA		145.0	0.0	.		143.0	57.0	0.399	NM_014789	A4FU80|B4DGP3|E7ENV5	Frame_Shift_Del	DEL	ENST00000501748.2	37	CCDS34957.1																																																																																			ATAAA|0.993;-|0.007	0.007	strong		0.415	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
MCCC1	56922	hgsc.bcm.edu	37	3	182755074	182755074	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182755074delC	ENST00000265594.4	-	13	1672	c.1526delG	c.(1525-1527)tgcfs	p.C509fs	MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000492597.1_Frame_Shift_Del_p.C400fs|MCCC1_ENST00000539926.1_Frame_Shift_Del_p.C374fs	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	509					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	GGCTGCCTGGCATAAAGACTC	0.507																																					p.C509fs		Pindel,Atlas-Indel	.											.	MCCC1	87	.	0			c.1527delC	GRCh37	CD053583	MCCC1	D		PASS	.						122.0	106.0	112.0					3																	182755074		2203	4300	6503	SO:0001589	frameshift_variant	56922	exon13			.	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1526delG	3.37:g.182755074delC	ENSP00000265594:p.Cys509fs	122.0	0.0	.		131.0	39.0	0.298	NM_020166	Q59ES4|Q9H959|Q9NS97	Frame_Shift_Del	DEL	ENST00000265594.4	37	CCDS3241.1																																																																																			.	.	none		0.507	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
SLC23A1	9963	hgsc.bcm.edu	37	5	138715033	138715034	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138715033_138715034insC	ENST00000348729.3	-	9	981_982	c.935_936insG	c.(934-936)ggcfs	p.G312fs	SLC23A1_ENST00000353963.3_Frame_Shift_Ins_p.G316fs|SLC23A1_ENST00000503919.1_5'Flank	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	312					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	CCGTGGGCAGGCCCCACTGACC	0.599																																					p.G316fs		Pindel,Atlas-Indel	.											.	SLC23A1	51	.	0			c.948_949insG						PASS	.																																			SO:0001589	frameshift_variant	9963	exon9			.	AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"""Solute carriers"""	10974	protein-coding gene	gene with protein product		603790	"""solute carrier family 23 (nucleobase transporters), member 2"""	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.936dupG	5.37:g.138715037_138715037dupC	ENSP00000302701:p.Gly312fs	85.0	0.0	.		99.0	16.0	0.162	NM_152685	O95191|Q8WWB6|Q9UGH4|Q9UI39	Frame_Shift_Ins	INS	ENST00000348729.3	37	CCDS4212.1																																																																																			.	.	none		0.599	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685	
RFC4	5984	hgsc.bcm.edu	37	3	186508121	186508122	+	Frame_Shift_Del	DEL	CA	CA	-	rs2066497	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186508121_186508122delCA	ENST00000392481.2	-	9	1156_1157	c.875_876delTG	c.(874-876)gtgfs	p.V293fs	SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000296273.2_Frame_Shift_Del_p.V293fs|RFC4_ENST00000433496.1_Intron	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	293					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		TTACCTTGACCACAGCTTCTAG	0.356																																					p.292_293del		Pindel,Atlas-Indel	.											RFC4,NS,carcinoma,+2,2	RFC4	54	2	0			c.876_877del						PASS	.																																			SO:0001589	frameshift_variant	5984	exon9			.		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.875_876delTG	3.37:g.186508123_186508124delCA	ENSP00000376272:p.Val293fs	134.0	0.0	.		112.0	24.0	0.214	NM_002916	B4DM41|D3DNV2|Q6FHX7	Frame_Shift_Del	DEL	ENST00000392481.2	37	CCDS3283.1																																																																																			.	.	none		0.356	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
KNOP1	400506	hgsc.bcm.edu	37	16	19725766	19725767	+	Frame_Shift_Ins	INS	-	-	C	rs532893765	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:19725766_19725767insC	ENST00000219837.7	-	2	669_670	c.591_592insG	c.(589-594)gggcagfs	p.Q198fs	AC002550.5_ENST00000565916.1_RNA|KNOP1_ENST00000568230.1_5'Flank|IQCK_ENST00000320394.6_5'Flank	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	198	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										TTCCGTTTCTGCCCCAAGGCTG	0.574																																					p.Q198fs		Pindel,Atlas-Indel	.											.	C16orf88	41	.	0			c.592_593insG						PASS	.																																			SO:0001589	frameshift_variant	400506	exon2			.	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.592dupG	16.37:g.19725770_19725770dupC	ENSP00000219837:p.Gln198fs	45.0	0.0	.		36.0	18.0	0.500	NM_001012991	O43328|Q5FWF3	Frame_Shift_Ins	INS	ENST00000219837.7	37	CCDS42127.1																																																																																			.	.	none		0.574	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991	
B2M	567	hgsc.bcm.edu	37	15	45007888	45007891	+	Frame_Shift_Del	DEL	TAGT	TAGT	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45007888_45007891delTAGT	ENST00000558401.1	+	2	405_408	c.335_338delTAGT	c.(334-339)atagttfs	p.IV112fs	B2M_ENST00000559220.1_Intron|B2M_ENST00000559916.1_Frame_Shift_Del_p.IV112fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.IV112fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	112	Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CAGCCCAAGATAGTTAAGTGGGGT	0.402																																					p.112_113del		Pindel	.											.	B2M	99	.	0			c.334_337del						PASS	.																																			SO:0001589	frameshift_variant	567	exon2			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.335_338delTAGT	15.37:g.45007888_45007891delTAGT	ENSP00000452780:p.Ile112fs	71.0	0.0	.		51.0	17.0	0.333	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.402	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949|rs199513201|rs199927874|rs150364859	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145586672_145586679delTTTTACAC	ENST00000334513.5	-	8	908_915	c.897_904delGTGTAAAA	c.(895-906)ccgtgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TAAGCTGCACTTTTACACGGTGGGGGTG	0.534																																					p.300_302del		Pindel	.											.	NUDT17	25	.	0			c.898_905del						PASS	.																																			SO:0001589	frameshift_variant	200035	exon8			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.897_904delGTGTAAAA	1.37:g.145586672_145586679delTTTTACAC	ENSP00000334437:p.Cys300fs	116.0	0.0	.		84.0	21.0	0.250	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			-|0.017;TTTTA|0.983	0.017	alt		0.534	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261306	+	Frame_Shift_Ins	INS	-	-	AACAAAC	rs202195469|rs200251419|rs565026588	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:29261305_29261306insAACAAAC	ENST00000399387.4	+	3	446_447	c.342_343insAACAAAC	c.(343-345)aaafs	p.K115fs	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						CTTCAGCACTAAAAAAAACAAA	0.376																																					.		Pindel	.											.	C14orf23	5	.	0			.						PASS	.																																			SO:0001589	frameshift_variant	387978	.			.			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	Exception_encountered	14.37:g.29261305_29261306insAACAAAC	ENSP00000382318:p.Lys115fs	86.0	0.0	.		67.0	12.0	0.179	.		RNA	INS	ENST00000399387.4	37																																																																																				-|0.668;AAC|0.332	.	alt		0.376	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
STK17B	9262	hgsc.bcm.edu	37	2	197004468	197004575	+	Splice_Site	DEL	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	-	rs567859155|rs140646128|rs374561119		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197004468_197004575delCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	ENST00000263955.4	-	7	943_998	c.657_712delTAAATGTTTAAAAATTAACATACATTTTAAGTTCCCCTCCCTTGTTTTTCAGGAATATTGGTATAATAGCATATATGTTGTTAACTCACACATCACCATTTGTGGGAG	c.(655-714)tgtaaatgtttaaaaattaacatacattttaagttcccctcccttgtttttcaggaatat>tgat	p.219_238CKCLKINIHFKFPSLVFQEY>*	STK17B_ENST00000409228.1_Splice_Site_p.219_238CKCLKINIHFKFPSLVFQEY>*	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	219	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			TGATTATCTTCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTATACAAAGTAC	0.315																																					p.219_238del		Pindel	.											.	STK17B	28	.	0			c.657_713del						PASS	.																																			SO:0001630	splice_region_variant	9262	exon7			.	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 2"""	604727	"""serine/threonine kinase 17b (apoptosis-inducing)"""			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.657-1TAAATGTTTAAAAATTAACATACATTTTAAGTTCCCCTCCCTTGTTTTTCAGGAATATTGGTATAATAGCATATATGTTGTTAACTCACACATCACCATTTGTGGGAG>-	2.37:g.197004468_197004575delCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA		84.0	0.0	.		68.0	15.0	0.221	NM_004226		In_Frame_Del	DEL	ENST00000263955.4	37	CCDS2315.1																																																																																			.	.	none		0.315	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		In_Frame_Del
SLC12A9	56996	hgsc.bcm.edu	37	7	100464136	100464136	+	Missense_Mutation	SNP	G	G	A	rs374047787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100464136G>A	ENST00000354161.3	+	14	2779	c.2654G>A	c.(2653-2655)cGc>cAc	p.R885H	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	885					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CGATACCCCCGCTACCTGGCG	0.677																																					p.R885H		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2654A						PASS	.	G	HIS/ARG	0,4368		0,0,2184	14.0	11.0	12.0		2654	0.4	0.0	7		12	1,8575		0,1,4287	no	missense	SLC12A9	NM_020246.2	29	0,1,6471	AA,AG,GG		0.0117,0.0,0.0077	benign	885/915	100464136	1,12943	2184	4288	6472	SO:0001583	missense	56996	exon14			ACCCCCGCTACCT	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.2654G>A	7.37:g.100464136G>A	ENSP00000275730:p.Arg885His	26.0	0.0	0		52.0	20.0	0.384615	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	G	3.991	-0.004508	0.07773	0.0	1.17E-4	ENSG00000146828	ENST00000354161	D	0.91124	-2.79	4.7	0.364	0.16124	.	0.285942	0.33591	N	0.004743	T	0.81814	0.4902	L	0.29908	0.895	0.24237	N	0.995379	B	0.09022	0.002	B	0.04013	0.001	T	0.68580	-0.5371	10	0.41790	T	0.15	.	7.9231	0.29859	0.4236:0.0:0.5764:0.0	.	885	Q9BXP2	S12A9_HUMAN	H	885	ENSP00000275730:R885H	ENSP00000275730:R885H	R	+	2	0	SLC12A9	100302072	0.000000	0.05858	0.003000	0.11579	0.014000	0.08584	0.153000	0.16323	-0.128000	0.11641	-0.378000	0.06908	CGC	.	.	weak		0.677	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
MN1	4330	hgsc.bcm.edu	37	22	28192809	28192809	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:28192809G>A	ENST00000302326.4	-	1	4677	c.3723C>T	c.(3721-3723)gaC>gaT	p.D1241D		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1241					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						ACGTCTTGTCGTCGTCCGCGC	0.607			T	ETV6	"""AML, meningioma"""																																p.D1241D		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	.	MN1	122	.	0			c.C3723T						PASS	.						91.0	97.0	95.0					22																	28192809		2149	4245	6394	SO:0001819	synonymous_variant	4330	exon1			CTTGTCGTCGTCC	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3723C>T	22.37:g.28192809G>A		81.0	0.0	0		96.0	30.0	0.3125	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	none		0.607	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
CLCA2	9635	hgsc.bcm.edu	37	1	86913384	86913384	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86913384T>A	ENST00000370565.4	+	11	2069	c.1907T>A	c.(1906-1908)cTt>cAt	p.L636H		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	636					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TATCCCATTCTTAATGCCACT	0.473																																					p.L636H	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.T1907A						PASS	.						107.0	103.0	104.0					1																	86913384		2203	4300	6503	SO:0001583	missense	9635	exon11			CCATTCTTAATGC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1907T>A	1.37:g.86913384T>A	ENSP00000359596:p.Leu636His	76.0	0.0	0		89.0	20.0	0.224719	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.271256	0.40194	.	.	ENSG00000137975	ENST00000370565	T	0.40476	1.03	5.82	2.13	0.27403	Domain of unknown function DUF1973 (1);	0.262170	0.31010	N	0.008430	T	0.38878	0.1057	M	0.87617	2.895	0.19300	N	0.99997	D	0.59767	0.986	P	0.53988	0.739	T	0.35847	-0.9772	10	0.62326	D	0.03	-5.1849	4.7281	0.12950	0.1189:0.0655:0.1245:0.691	.	636	Q9UQC9	CLCA2_HUMAN	H	636	ENSP00000359596:L636H	ENSP00000359596:L636H	L	+	2	0	CLCA2	86685972	0.998000	0.40836	0.817000	0.32601	0.287000	0.27160	2.049000	0.41288	0.100000	0.17581	-0.316000	0.08728	CTT	.	.	none		0.473	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
RRP8	23378	hgsc.bcm.edu	37	11	6622218	6622218	+	Missense_Mutation	SNP	G	G	A	rs17834692	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6622218G>A	ENST00000254605.6	-	4	1102	c.985C>T	c.(985-987)Cct>Tct	p.P329S	RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank|RRP8_ENST00000534343.1_Intron	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	329			P -> S (in dbSNP:rs17834692).		cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						CAATGCACAGGGTTCCGGATA	0.552													G|||	151	0.0301518	0.0045	0.0836	5008	,	,		20815	0.0109		0.008	False		,,,				2504	0.0695				p.P329S		Atlas-SNP	.											.	RRP8	40	.	0			c.C985T						PASS	.	G	SER/PRO	43,4359	45.3+/-79.5	0,43,2158	104.0	103.0	104.0		985	2.2	1.0	11	dbSNP_123	104	68,8524	40.8+/-97.7	0,68,4228	yes	missense	RRP8	NM_015324.3	74	0,111,6386	AA,AG,GG		0.7914,0.9768,0.8542	benign	329/457	6622218	111,12883	2201	4296	6497	SO:0001583	missense	23378	exon4			GCACAGGGTTCCG	AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"""KIAA0409"""	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.985C>T	11.37:g.6622218G>A	ENSP00000254605:p.Pro329Ser	60.0	0.0	0		91.0	39.0	0.428571	NM_015324	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	43	0.019688644688644688	1	0.0020325203252032522	24	0.06629834254143646	11	0.019230769230769232	7	0.009234828496042216	G	10.87	1.472472	0.26423	0.009768	0.007914	ENSG00000132275	ENST00000254605	T	0.39229	1.09	5.41	2.22	0.28083	.	0.387563	0.27500	N	0.019093	T	0.01287	0.0042	N	0.01576	-0.805	0.80722	D	1	B	0.18166	0.026	B	0.19666	0.026	T	0.05131	-1.0904	10	0.40728	T	0.16	0.8153	14.0765	0.64893	0.0:0.0:0.4887:0.5113	rs17834692;rs52826857;rs17834692	329	O43159	RRP8_HUMAN	S	329	ENSP00000254605:P329S	ENSP00000254605:P329S	P	-	1	0	RRP8	6578794	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	1.286000	0.33273	0.796000	0.33947	0.655000	0.94253	CCT	G|0.986;A|0.014	0.014	strong		0.552	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324	
ALDH3A2	224	hgsc.bcm.edu	37	17	19575096	19575096	+	Missense_Mutation	SNP	C	C	T	rs61737992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:19575096C>T	ENST00000176643.6	+	9	1716	c.1270C>T	c.(1270-1272)Ccc>Tcc	p.P424S	ALDH3A2_ENST00000579855.1_Missense_Mutation_p.P424S|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.P424S|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.P424S|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.P424S|ALDH3A2_ENST00000571163.1_Intron			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	424					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					TCATCAGCGTCCCTGTTTATT	0.388													C|||	12	0.00239617	0.0	0.0058	5008	,	,		18840	0.0		0.007	False		,,,				2504	0.001				p.P424S		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C1270T						PASS	.	C	SER/PRO,SER/PRO	2,4404	4.2+/-10.8	0,2,2201	104.0	110.0	108.0		1270,1270	-1.8	0.7	17	dbSNP_129	108	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	ALDH3A2	NM_000382.2,NM_001031806.1	74,74	0,60,6443	TT,TC,CC		0.6744,0.0454,0.4613	benign,benign	424/486,424/509	19575096	60,12946	2203	4300	6503	SO:0001583	missense	224	exon9			CAGCGTCCCTGTT	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"""Aldehyde dehydrogenases"""	403	protein-coding gene	gene with protein product	"""fatty aldehyde dehydrogenase"""	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.1270C>T	17.37:g.19575096C>T	ENSP00000176643:p.Pro424Ser	102.0	0.0	0		104.0	50.0	0.480769	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	2.583	-0.296965	0.05532	4.54E-4	0.006744	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	D;D;D	0.83591	-1.74;-1.74;-1.74	6.06	-1.82	0.07857	Aldehyde/histidinol dehydrogenase (1);	0.872349	0.10601	N	0.655669	T	0.46852	0.1414	N	0.02830	-0.485	0.43603	D	0.99596	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.51172	-0.8739	10	0.02654	T	1	-4.9546	8.2837	0.31915	0.0:0.1298:0.4471:0.423	rs61737992	424;424	P51648;P51648-2	AL3A2_HUMAN;.	S	424	ENSP00000176643:P424S;ENSP00000378942:P424S;ENSP00000345774:P424S	ENSP00000176643:P424S	P	+	1	0	ALDH3A2	19515688	0.000000	0.05858	0.736000	0.30914	0.993000	0.82548	-0.852000	0.04308	-0.339000	0.08401	0.650000	0.86243	CCC	C|0.996;T|0.004	0.004	strong		0.388	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1		
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739922	20739922	+	Nonsense_Mutation	SNP	G	G	A	rs555447511	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:20739922G>A	ENST00000427390.2	-	8	1918	c.1828C>T	c.(1828-1830)Cag>Tag	p.Q610*		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	610	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						ttctcctcctgcttccacatc	0.557													G|||	165	0.0329473	0.0023	0.1066	5008	,	,		21619	0.003		0.0467	False		,,,				2504	0.0389				p.Q610X		Atlas-SNP	.											.	GOLGA6L6	37	.	0			c.C1828T						PASS	.						6.0	5.0	5.0					15																	20739922		618	1440	2058	SO:0001587	stop_gained	727832	exon8			CCTCCTGCTTCCA	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1828C>T	15.37:g.20739922G>A	ENSP00000398615:p.Gln610*	61.0	0.0	0		87.0	47.0	0.54023	NM_001145004	D3YTC0	Nonsense_Mutation	SNP	ENST00000427390.2	37	CCDS45184.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.326772	0.60743	.	.	ENSG00000215405	ENST00000427390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	.	.	.	.	.	.	.	X	610	.	ENSP00000398615:Q610X	Q	-	1	0	GOLGA6L6	18999936	0.000000	0.05858	0.033000	0.17914	0.033000	0.12548	0.046000	0.14035	0.159000	0.19401	0.162000	0.16502	CAG	.	.	none		0.557	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
MT-ND6	4541	hgsc.bcm.edu	37	M	14149	14149	+	Splice_Site	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrM:14149C>T	ENST00000361681.2	-	1	524	c.525G>A	c.(523-525)agG>agA	p.R175R	MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	0					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						TAATCACATAACCTATTCCCC	0.408																																					p.X175X		Atlas-SNP	.											.	.	.	.	0			c.G525A						PASS	.																																			SO:0001630	splice_region_variant	0	exon1			ACATAACCTATTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.525+1G>A	M.37:g.14149C>T		12.0	0.0	0		19.0	19.0	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				A|0.995;G|0.005	.	alt		0.408	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	Silent
SFMBT2	57713	hgsc.bcm.edu	37	10	7412243	7412243	+	Splice_Site	SNP	G	G	A	rs142871492	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:7412243G>A	ENST00000361972.4	-	3	285	c.195C>T	c.(193-195)caC>caT	p.H65H	SFMBT2_ENST00000397167.1_Splice_Site_p.H65H|SFMBT2_ENST00000379711.2_Splice_Site_p.H65H|SFMBT2_ENST00000397160.3_Splice_Site_p.H65H|SFMBT2_ENST00000379713.3_Splice_Site_p.H65H	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	65					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CTTTACATACGTGTTTGAATG	0.473													G|||	3	0.000599042	0.0015	0.0	5008	,	,		20525	0.0		0.001	False		,,,				2504	0.0				p.H65H		Atlas-SNP	.											.	SFMBT2	209	.	0			c.C195T						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	118.0	107.0	111.0		195,195	-6.2	0.8	10	dbSNP_134	111	38,8562	26.3+/-74.7	0,38,4262	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SFMBT2	NM_001018039.1,NM_001029880.2	,	0,44,6459	AA,AG,GG		0.4419,0.1362,0.3383	,	65/895,65/895	7412243	44,12962	2203	4300	6503	SO:0001630	splice_region_variant	57713	exon3			ACATACGTGTTTG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.195+1C>T	10.37:g.7412243G>A		119.0	0.0	0		73.0	32.0	0.438356	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																			G|0.997;A|0.003	0.003	strong		0.473	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	Silent
ACP6	51205	hgsc.bcm.edu	37	1	147131611	147131611	+	Missense_Mutation	SNP	C	C	T	rs144959805	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:147131611C>T	ENST00000369238.6	-	3	826	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	ACP6_ENST00000392988.2_Missense_Mutation_p.V127M	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	127	Substrate binding. {ECO:0000250}.				dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					TGCATGCCCACCTTGGTCAGC	0.488													C|||	2	0.000399361	0.0	0.0	5008	,	,		22613	0.0		0.002	False		,,,				2504	0.0				p.V127M		Atlas-SNP	.											.	ACP6	36	.	0			c.G379A						PASS	.	C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	97.0	90.0	92.0		379	4.7	1.0	1	dbSNP_134	92	9,8591	7.1+/-27.0	0,9,4291	yes	missense	ACP6	NM_016361.3	21	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	probably-damaging	127/429	147131611	11,12995	2203	4300	6503	SO:0001583	missense	51205	exon3			TGCCCACCTTGGT	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.379G>A	1.37:g.147131611C>T	ENSP00000358241:p.Val127Met	69.0	0.0	0		124.0	61.0	0.491935	NM_016361	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Missense_Mutation	SNP	ENST00000369238.6	37	CCDS928.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.37	3.814172	0.70912	4.54E-4	0.001047	ENSG00000162836	ENST00000369238;ENST00000392988	T;T	0.30182	1.54;1.54	5.66	4.72	0.59763	.	0.253086	0.41605	D	0.000858	T	0.45558	0.1348	M	0.72479	2.2	0.45806	D	0.998685	D;D	0.62365	0.989;0.991	P;D	0.67103	0.768;0.949	T	0.34079	-0.9843	10	0.48119	T	0.1	.	15.9939	0.80228	0.1351:0.8649:0.0:0.0	.	127;127	Q9NPH0-2;Q9NPH0	.;PPA6_HUMAN	M	127	ENSP00000358241:V127M;ENSP00000376714:V127M	ENSP00000358241:V127M	V	-	1	0	ACP6	145598235	0.599000	0.26891	0.965000	0.40720	0.996000	0.88848	1.076000	0.30729	2.656000	0.90262	0.655000	0.94253	GTG	C|0.999;T|0.001	0.001	strong		0.488	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361	
CEACAM1	634	hgsc.bcm.edu	37	19	43031318	43031318	+	Missense_Mutation	SNP	G	G	A	rs199627333		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43031318G>A	ENST00000161559.6	-	2	433	c.299C>T	c.(298-300)aCa>aTa	p.T100I	CEACAM1_ENST00000358394.3_Missense_Mutation_p.T100I|CEACAM1_ENST00000308072.4_Missense_Mutation_p.T60I|CEACAM1_ENST00000351134.3_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000352591.5_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000599389.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000403444.3_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000594688.1_RNA	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	100	Ig-like V-type.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	GGGGTATATTGTCTCTCGACC	0.473																																					p.T100I		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C299T						PASS	.						358.0	304.0	322.0					19																	43031318		2203	4300	6503	SO:0001583	missense	634	exon2			TATATTGTCTCTC	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.299C>T	19.37:g.43031318G>A	ENSP00000161559:p.Thr100Ile	275.0	0.0	0		313.0	13.0	0.0415335	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	g	8.472	0.857824	0.17178	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	4.41	-0.431	0.12295	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46737	0.1408	L	0.33485	1.01	0.09310	N	1	B;B;B;B;B;B;B;B;B;B	0.31989	0.35;0.005;0.001;0.003;0.001;0.005;0.197;0.012;0.022;0.054	B;B;B;B;B;B;B;B;B;B	0.30495	0.103;0.005;0.003;0.006;0.002;0.01;0.116;0.007;0.051;0.026	T	0.26710	-1.0095	9	0.24483	T	0.36	.	3.4213	0.07395	0.1214:0.1385:0.5979:0.1422	.	100;100;100;100;100;100;100;100;100;100	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	I	100;100;100;127;60;100;100;100;60;100;100;100	ENSP00000161559:T100I;ENSP00000351165:T100I;ENSP00000325946:T100I;ENSP00000244291:T100I;ENSP00000384709:T100I;ENSP00000384083:T100I;ENSP00000312184:T60I	ENSP00000161559:T100I	T	-	2	0	CEACAM1	47723158	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-1.426000	0.02443	-0.044000	0.13491	-2.357000	0.00240	ACA	.	.	weak		0.473	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
CYP3A4	1576	hgsc.bcm.edu	37	7	99358598	99358598	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358598G>A	ENST00000336411.2	-	12	1443	c.1260C>T	c.(1258-1260)agC>agT	p.S420S	CYP3A4_ENST00000354593.2_Silent_p.S270S	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	420					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	TGTTCTTCTTGCTGAATCTGG	0.413																																					p.S420S		Atlas-SNP	.											.	CYP3A4	56	.	0			c.C1260T						PASS	.						375.0	327.0	343.0					7																	99358598		2203	4300	6503	SO:0001819	synonymous_variant	1576	exon12			CTTCTTGCTGAAT	AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"""Cytochrome P450s"""	2637	protein-coding gene	gene with protein product		124010	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"""	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.1260C>T	7.37:g.99358598G>A		276.0	0.0	0		252.0	105.0	0.416667	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1		
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	153.0	1.0	0.00653595		178.0	9.0	0.0505618	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
CDH8	1006	hgsc.bcm.edu	37	16	61935317	61935317	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:61935317C>A	ENST00000577390.1	-	3	1267	c.313G>T	c.(313-315)Gct>Tct	p.A105S	CDH8_ENST00000577730.1_Missense_Mutation_p.A105S|CDH8_ENST00000299345.6_Missense_Mutation_p.A105S|CDH8_ENST00000584337.1_Missense_Mutation_p.A105S	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	105	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATGGTCCCAGCTCCATCACCT	0.408																																					p.A105S		Atlas-SNP	.											CDH8,NS,carcinoma,0,1	CDH8	273	1	0			c.G313T						PASS	.						105.0	100.0	102.0					16																	61935317		2203	4300	6503	SO:0001583	missense	1006	exon3			TCCCAGCTCCATC	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.313G>T	16.37:g.61935317C>A	ENSP00000462701:p.Ala105Ser	87.0	0.0	0		98.0	20.0	0.204082	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	31	5.096254	0.94197	.	.	ENSG00000150394	ENST00000299345	T	0.49720	0.77	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.097389	0.64402	D	0.000001	T	0.70727	0.3257	M	0.70842	2.15	0.80722	D	1	P	0.43826	0.818	D	0.64144	0.922	T	0.67929	-0.5543	10	0.66056	D	0.02	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	105	P55286	CADH8_HUMAN	S	105	ENSP00000299345:A105S	ENSP00000299345:A105S	A	-	1	0	CDH8	60492818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	GCT	.	.	none		0.408	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
UMODL1	89766	hgsc.bcm.edu	37	21	43557637	43557637	+	Silent	SNP	C	C	T	rs200233807	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43557637C>T	ENST00000408910.2	+	22	3864	c.3864C>T	c.(3862-3864)gcC>gcT	p.A1288A	UMODL1_ENST00000400424.2_Silent_p.A1216A|UMODL1_ENST00000408989.2_Silent_p.A1416A|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Silent_p.A1344A	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1288					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CGGGAACAGCCACCCTTCTGA	0.547													C|||	3	0.000599042	0.0	0.0	5008	,	,		15307	0.0		0.002	False		,,,				2504	0.001				p.A1416A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C4248T						PASS	.	C	,,,	1,4129		0,1,2064	149.0	157.0	154.0		3864,4032,3648,4248	-6.1	0.0	21		154	14,8372		0,14,4179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,15,6243	TT,TC,CC		0.1669,0.0242,0.1198	,,,	1288/1319,1344/1375,1216/1247,1416/1447	43557637	15,12501	2065	4193	6258	SO:0001819	synonymous_variant	89766	exon21			AACAGCCACCCTT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3864C>T	21.37:g.43557637C>T		131.0	0.0	0		205.0	127.0	0.619512	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
CENPB	1059	hgsc.bcm.edu	37	20	3766137	3766137	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3766137G>T	ENST00000379751.4	-	1	1200	c.994C>A	c.(994-996)Cag>Aag	p.Q332K	CDC25B_ENST00000344256.6_5'Flank|CDC25B_ENST00000379598.5_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	332					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						CCCTTCACCTGCTGGACCACT	0.682																																					p.Q332K		Atlas-SNP	.											.	CENPB	24	.	0			c.C994A						PASS	.						18.0	16.0	17.0					20																	3766137		2199	4293	6492	SO:0001583	missense	1059	exon1			TCACCTGCTGGAC	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"""centromere protein B (80kD)"""			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.994C>A	20.37:g.3766137G>T	ENSP00000369075:p.Gln332Lys	88.0	0.0	0		73.0	35.0	0.479452	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	37	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	g	14.57	2.576145	0.45902	.	.	ENSG00000125817	ENST00000379751	T	0.41065	1.01	4.04	4.04	0.47022	.	0.000000	0.35646	U	0.003063	T	0.32645	0.0836	L	0.36672	1.1	0.32344	N	0.559389	B	0.28258	0.205	B	0.19148	0.024	T	0.48456	-0.9034	10	0.56958	D	0.05	-12.9621	13.6906	0.62544	0.0:0.0:1.0:0.0	.	332	P07199	CENPB_HUMAN	K	332	ENSP00000369075:Q332K	ENSP00000369075:Q332K	Q	-	1	0	CENPB	3714137	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	2.752000	0.47516	1.801000	0.52704	0.457000	0.33378	CAG	.	.	none		0.682	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810	
AMER1	139285	hgsc.bcm.edu	37	X	63412987	63412987	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:63412987A>G	ENST00000330258.3	-	2	452	c.180T>C	c.(178-180)ttT>ttC	p.F60F	AMER1_ENST00000374869.3_Silent_p.F60F|AMER1_ENST00000403336.1_Silent_p.F60F	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	60					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TCTTGCCACCAAAGAGTTTCA	0.532																																					p.F60F		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T180C						PASS	.						181.0	147.0	159.0					X																	63412987		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			GCCACCAAAGAGT	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.180T>C	X.37:g.63412987A>G		73.0	0.0	0		123.0	51.0	0.414634	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			.	.	none		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
FCF1	51077	hgsc.bcm.edu	37	14	75190002	75190002	+	Missense_Mutation	SNP	T	T	C	rs41309250	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:75190002T>C	ENST00000341162.4	+	5	374	c.320T>C	c.(319-321)aTg>aCg	p.M107T	FCF1_ENST00000534938.2_Missense_Mutation_p.M95T|FCF1_ENST00000553615.1_Missense_Mutation_p.M92T	NM_015962.4	NP_057046.1	Q9Y324	FCF1_HUMAN	FCF1 rRNA-processing protein	107	PINc.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.0037)		GATTGTGTAATGGCTGAAATT	0.388													T|||	15	0.00299521	0.0	0.0115	5008	,	,		15747	0.0		0.002	False		,,,				2504	0.0051				p.M107T		Atlas-SNP	.											.	FCF1	15	.	0			c.T320C						PASS	.	T	THR/MET	5,4401	9.9+/-24.2	0,5,2198	117.0	111.0	113.0		320	6.1	1.0	14	dbSNP_127	113	39,8561	26.8+/-75.7	0,39,4261	yes	missense	FCF1	NM_015962.4	81	0,44,6459	CC,CT,TT		0.4535,0.1135,0.3383	possibly-damaging	107/199	75190002	44,12962	2203	4300	6503	SO:0001583	missense	51077	exon5			GTGTAATGGCTGA	AF132969	CCDS9832.1	14q24.2	2013-05-03	2013-05-03	2007-01-30	ENSG00000119616	ENSG00000119616			20220	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 111"", ""FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)"""	C14orf111		16762320	Standard	XR_245690		Approved	CGI-35, Bka, UTP24	uc001xqh.3	Q9Y324		ENST00000341162.4:c.320T>C	14.37:g.75190002T>C	ENSP00000344393:p.Met107Thr	115.0	0.0	0		122.0	67.0	0.54918	NM_015962	Q86TW8|Q8TBL8	Missense_Mutation	SNP	ENST00000341162.4	37	CCDS9832.1	7	0.003205128205128205	0	0.0	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	26.4	4.738739	0.89573	0.001135	0.004535	ENSG00000119616	ENST00000554590;ENST00000341162;ENST00000534938;ENST00000553615	.	.	.	6.06	6.06	0.98353	Nucleotide binding protein, PINc (1);	0.034297	0.85682	D	0.000000	T	0.72914	0.3520	H	0.96175	3.78	0.80722	D	1	P;B	0.37015	0.578;0.159	P;B	0.45712	0.491;0.257	D	0.83359	0.0001	9	0.66056	D	0.02	.	16.6093	0.84858	0.0:0.0:0.0:1.0	rs41309250	107;92	Q9Y324;G3V5S9	FCF1_HUMAN;.	T	18;107;95;92	.	ENSP00000344393:M107T	M	+	2	0	FCF1	74259755	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.760000	0.85248	2.324000	0.78689	0.533000	0.62120	ATG	T|0.995;C|0.005	0.005	strong		0.388	FCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413622.1	NM_015962	
UPP2	151531	hgsc.bcm.edu	37	2	158991346	158991346	+	Missense_Mutation	SNP	C	C	T	rs144945330	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:158991346C>T	ENST00000005756.4	+	7	1092	c.898C>T	c.(898-900)Cgg>Tgg	p.R300W	UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Missense_Mutation_p.R357W|UPP2_ENST00000605860.1_Missense_Mutation_p.R357W|UPP2-IT1_ENST00000439185.1_RNA	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	300					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	GTACCAGCAACGGCCTCAGCT	0.527																																					p.R357W		Atlas-SNP	.											.	UPP2	60	.	0			c.C1069T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	170.0	149.0	156.0		1069,898	1.1	0.2	2	dbSNP_134	156	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	UPP2	NM_001135098.1,NM_173355.3	101,101	0,10,6493	TT,TC,CC		0.093,0.0454,0.0769	probably-damaging,probably-damaging	357/375,300/318	158991346	10,12996	2203	4300	6503	SO:0001583	missense	151531	exon9			CAGCAACGGCCTC	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.898C>T	2.37:g.158991346C>T	ENSP00000005756:p.Arg300Trp	138.0	0.0	0		91.0	20.0	0.21978	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111302	0.37242	4.54E-4	9.3E-4	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.88277	-2.36;-2.36	4.94	1.14	0.20703	Nucleoside phosphorylase domain (1);	0.237699	0.41938	N	0.000790	D	0.93383	0.7890	M	0.90019	3.08	0.52099	D	0.999941	D	0.89917	1.0	D	0.97110	1.0	D	0.89713	0.3913	10	0.72032	D	0.01	.	3.7355	0.08508	0.1699:0.5569:0.0:0.2731	.	300	O95045	UPP2_HUMAN	W	357;300	ENSP00000387230:R357W;ENSP00000005756:R300W	ENSP00000005756:R300W	R	+	1	2	UPP2	158699592	0.971000	0.33674	0.241000	0.24154	0.212000	0.24457	0.214000	0.17541	0.029000	0.15352	-1.100000	0.02121	CGG	C|0.999;T|0.001	0.001	strong		0.527	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
LRP1	4035	hgsc.bcm.edu	37	12	57603636	57603636	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:57603636C>T	ENST00000243077.3	+	80	12890	c.12424C>T	c.(12424-12426)Cac>Tac	p.H4142Y		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4142					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TTACCATCAGCACAAGCAGCC	0.607																																					p.H4142Y		Atlas-SNP	.											.	LRP1	428	.	0			c.C12424T						PASS	.						45.0	46.0	46.0					12																	57603636		2203	4300	6503	SO:0001583	missense	4035	exon80			CATCAGCACAAGC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12424C>T	12.37:g.57603636C>T	ENSP00000243077:p.His4142Tyr	47.0	0.0	0		49.0	18.0	0.367347	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	5.539	0.284349	0.10513	.	.	ENSG00000123384	ENST00000243077	T	0.24723	1.84	4.45	4.45	0.53987	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.078423	0.52532	D	0.000071	T	0.05410	0.0143	N	0.00483	-1.445	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35798	-0.9774	10	0.02654	T	1	.	6.8782	0.24158	0.0:0.8089:0.0:0.1911	.	4142	Q07954	LRP1_HUMAN	Y	4142	ENSP00000243077:H4142Y	ENSP00000243077:H4142Y	H	+	1	0	LRP1	55889903	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.699000	0.54778	2.486000	0.83907	0.557000	0.71058	CAC	.	.	none		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CCND3	896	hgsc.bcm.edu	37	6	41909273	41909273	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41909273C>T	ENST00000372991.4	-	1	313	c.115G>A	c.(115-117)Gta>Ata	p.V39I	CCND3_ENST00000511642.1_Intron|CCND3_ENST00000415497.2_Intron|CCND3_ENST00000511686.1_Intron|CCND3_ENST00000372988.4_Intron|CCND3_ENST00000414200.2_Missense_Mutation_p.V39I|CCND3_ENST00000372987.4_5'Flank|CCND3_ENST00000510503.1_Intron	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	39	Cyclin N-terminal.				cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(13)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	20	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCGCGGGGTACGTAGCGCTCC	0.706			T	IGH@	MM																																p.V39I		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	.	CCND3	40	.	0			c.G115A						PASS	.						18.0	19.0	19.0					6																	41909273		2202	4297	6499	SO:0001583	missense	896	exon1			GGGGTACGTAGCG		CCDS4863.1, CCDS47425.1, CCDS47426.1, CCDS47427.1, CCDS75452.1	6p21	2008-08-26			ENSG00000112576	ENSG00000112576			1585	protein-coding gene	gene with protein product		123834				1386335	Standard	NM_001136125		Approved		uc003orn.3	P30281	OTTHUMG00000014690	ENST00000372991.4:c.115G>A	6.37:g.41909273C>T	ENSP00000362082:p.Val39Ile	104.0	0.0	0		72.0	22.0	0.305556	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Missense_Mutation	SNP	ENST00000372991.4	37	CCDS4863.1	.	.	.	.	.	.	.	.	.	.	c	13.50	2.255643	0.39896	.	.	ENSG00000112576	ENST00000372991;ENST00000414200	T;T	0.41758	2.82;0.99	3.15	2.2	0.27929	Cyclin, N-terminal (1);Cyclin-like (1);	0.986976	0.08207	U	0.981311	T	0.22859	0.0552	N	0.24115	0.695	0.80722	D	1	D;B;B	0.57899	0.981;0.079;0.006	P;B;B	0.62184	0.899;0.018;0.007	T	0.51116	-0.8746	10	0.19147	T	0.46	.	1.6151	0.02701	0.2449:0.4433:0.1833:0.1285	.	39;39;39	B4DRB9;E9PAS4;P30281	.;.;CCND3_HUMAN	I	39	ENSP00000362082:V39I;ENSP00000397545:V39I	ENSP00000362082:V39I	V	-	1	0	CCND3	42017251	0.000000	0.05858	1.000000	0.80357	0.772000	0.43724	0.043000	0.13971	0.568000	0.29311	0.313000	0.20887	GTA	.	.	none		0.706	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760	
ANKRD1	27063	hgsc.bcm.edu	37	10	92679979	92679979	+	Missense_Mutation	SNP	G	G	C	rs397517248		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:92679979G>C	ENST00000371697.3	-	2	402	c.154C>G	c.(154-156)Cct>Gct	p.P52A	RNU6-740P_ENST00000364734.1_RNA	NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	52					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				AGGGTCACAGGGTGGGCTAGA	0.527																																					p.P52A		Atlas-SNP	.											.	ANKRD1	50	.	0			c.C154G						PASS	.						217.0	207.0	210.0					10																	92679979		2203	4300	6503	SO:0001583	missense	27063	exon2			TCACAGGGTGGGC	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"""Ankyrin repeat domain containing"""	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.154C>G	10.37:g.92679979G>C	ENSP00000360762:p.Pro52Ala	144.0	0.0	0		147.0	71.0	0.482993	NM_014391	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	37	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	G	0.736	-0.778119	0.02929	.	.	ENSG00000148677	ENST00000371697	T	0.65178	-0.14	5.76	0.17	0.15021	.	1.015060	0.07860	N	0.966081	T	0.39172	0.1068	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25047	-1.0143	10	0.44086	T	0.13	.	6.7379	0.23419	0.4033:0.0:0.4791:0.1176	.	52	Q15327	ANKR1_HUMAN	A	52	ENSP00000360762:P52A	ENSP00000360762:P52A	P	-	1	0	ANKRD1	92669959	0.003000	0.15002	0.025000	0.17156	0.275000	0.26752	0.012000	0.13287	0.053000	0.16036	0.650000	0.86243	CCT	.	.	none		0.527	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391	
ZFAND2B	130617	hgsc.bcm.edu	37	2	220072382	220072382	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220072382C>T	ENST00000289528.5	+	3	358	c.163C>T	c.(163-165)Cct>Tct	p.P55S	ZFAND2B_ENST00000409206.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409412.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409319.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.P55S	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	55						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TATCCAGGTACCTGTGTGCCC	0.557																																					p.P55S		Atlas-SNP	.											ZFAND2B_ENST00000444522,NS,carcinoma,-1,2	ZFAND2B	28	2	0			c.C163T						PASS	.						97.0	86.0	90.0					2																	220072382		2203	4300	6503	SO:0001583	missense	130617	exon3			CAGGTACCTGTGT	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.163C>T	2.37:g.220072382C>T	ENSP00000289528:p.Pro55Ser	80.0	0.0	0		82.0	28.0	0.341463	NM_138802	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	37	CCDS2435.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033810	0.93575	.	.	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409412;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000409319;ENST00000444522	T;T;T;T;T;T;T;T;T;T	0.49432	0.88;0.88;0.78;0.83;0.93;0.81;0.78;0.81;0.93;0.81	5.17	5.17	0.71159	Zinc finger, AN1-type (1);	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.96;0.994	T	0.82063	-0.0643	10	0.62326	D	0.03	-17.9994	18.4617	0.90741	0.0:1.0:0.0:0.0	.	55;55	Q8WV99;B4DEN4	ZFN2B_HUMAN;.	S	55	ENSP00000386824:P55S;ENSP00000386399:P55S;ENSP00000289528:P55S;ENSP00000409931:P55S;ENSP00000386847:P55S;ENSP00000387179:P55S;ENSP00000386898:P55S;ENSP00000386370:P55S;ENSP00000387312:P55S;ENSP00000411334:P55S	ENSP00000289528:P55S	P	+	1	0	ZFAND2B	219780626	1.000000	0.71417	0.982000	0.44146	0.998000	0.95712	7.080000	0.76837	2.691000	0.91804	0.655000	0.94253	CCT	.	.	none		0.557	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
ZNF646	9726	hgsc.bcm.edu	37	16	31090221	31090221	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31090221C>T	ENST00000394979.2	+	1	2999	c.2576C>T	c.(2575-2577)tCt>tTt	p.S859F	ZNF646_ENST00000300850.5_Missense_Mutation_p.S859F			O15015	ZN646_HUMAN	zinc finger protein 646	859					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						GAGTTTGACTCTCTGCCTGCC	0.622																																					p.S859F		Atlas-SNP	.											.	ZNF646	133	.	0			c.C2576T						PASS	.						67.0	73.0	71.0					16																	31090221		2197	4300	6497	SO:0001583	missense	9726	exon2			TTGACTCTCTGCC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.2576C>T	16.37:g.31090221C>T	ENSP00000378429:p.Ser859Phe	83.0	0.0	0		91.0	4.0	0.043956	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	C	17.73	3.462089	0.63513	.	.	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.79247	-1.25;-1.25	5.1	5.1	0.69264	.	.	.	.	.	T	0.79834	0.4514	L	0.38175	1.15	0.32404	N	0.551577	D	0.76494	0.999	D	0.73380	0.98	T	0.78309	-0.2254	9	0.26408	T	0.33	-11.2798	8.9229	0.35623	0.1657:0.6738:0.1604:0.0	.	859	O15015-2	.	F	859	ENSP00000300850:S859F;ENSP00000378429:S859F	ENSP00000300850:S859F	S	+	2	0	ZNF646	30997722	0.882000	0.30256	1.000000	0.80357	0.997000	0.91878	1.968000	0.40500	2.380000	0.81148	0.563000	0.77884	TCT	.	.	none		0.622	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
STAB1	23166	hgsc.bcm.edu	37	3	52557136	52557136	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:52557136T>G	ENST00000321725.6	+	63	7082	c.7006T>G	c.(7006-7008)Tcc>Gcc	p.S2336A		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2336	FAS1 7. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TGCCAACTTCTCCACCTTCTA	0.627																																					p.S2336A		Atlas-SNP	.											.	STAB1	178	.	0			c.T7006G						PASS	.						70.0	74.0	73.0					3																	52557136		2202	4299	6501	SO:0001583	missense	23166	exon63			AACTTCTCCACCT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.7006T>G	3.37:g.52557136T>G	ENSP00000312946:p.Ser2336Ala	61.0	0.0	0		54.0	5.0	0.0925926	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535227	0.85812	.	.	ENSG00000010327	ENST00000321725	D	0.93604	-3.25	5.74	5.74	0.90152	FAS1 domain (3);	0.000000	0.85682	D	0.000000	D	0.95711	0.8605	M	0.62016	1.91	0.47547	D	0.999452	D;D	0.76494	0.999;0.994	D;P	0.68192	0.956;0.893	D	0.95543	0.8614	10	0.49607	T	0.09	.	15.7088	0.77609	0.0:0.0:0.0:1.0	.	223;2336	B3KSK0;Q9NY15	.;STAB1_HUMAN	A	2336	ENSP00000312946:S2336A	ENSP00000312946:S2336A	S	+	1	0	STAB1	52532176	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.595000	0.61048	2.190000	0.69967	0.459000	0.35465	TCC	.	.	none		0.627	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
FHIT	2272	hgsc.bcm.edu	37	3	60522657	60522657	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:60522657A>C	ENST00000468189.1	-	5	409	c.39T>G	c.(37-39)tcT>tcG	p.S13S	FHIT_ENST00000341848.4_Silent_p.S13S|FHIT_ENST00000492590.1_Silent_p.S13S|FHIT_ENST00000476844.1_Silent_p.S13S			P49789	FHIT_HUMAN	fragile histidine triad	13	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				DNA replication (GO:0006260)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide metabolic process (GO:0009117)|purine nucleotide metabolic process (GO:0006163)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|catalytic activity (GO:0003824)|hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)	12		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		GAAACACTACAGAGGGCTTGA	0.373			T	HMGA2	pleomorphic salivary gland adenoma				Renal Cell Cancer associated with constitutional translocation of chromosome 3																												p.S13S		Atlas-SNP	.		Dom	yes		3	3p14.2	2272	fragile histidine triad gene		E	.	FHIT	44	.	0			c.T39G						PASS	.						96.0	89.0	92.0					3																	60522657		2203	4300	6503	SO:0001819	synonymous_variant	2272	exon5	Familial Cancer Database		CACTACAGAGGGC	BC032336	CCDS2894.1	3p14.2	2012-02-27	2012-02-27		ENSG00000189283	ENSG00000189283			3701	protein-coding gene	gene with protein product		601153	"""fragile histidine triad gene"""			8598045, 9671749	Standard	NM_002012		Approved	FRA3B, AP3Aase	uc003dky.3	P49789	OTTHUMG00000158591	ENST00000468189.1:c.39T>G	3.37:g.60522657A>C		42.0	0.0	0		59.0	13.0	0.220339	NM_002012	A2IAS9|A2IAT0|A2IAT6|A8K1A9|Q45QG9|Q6IU12	Silent	SNP	ENST00000468189.1	37	CCDS2894.1																																																																																			.	.	none		0.373	FHIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351648.1	NM_002012	
CSMD1	64478	hgsc.bcm.edu	37	8	3019696	3019696	+	Silent	SNP	G	G	A	rs145598896	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:3019696G>A	ENST00000520002.1	-	39	6387	c.5832C>T	c.(5830-5832)ccC>ccT	p.P1944P	CSMD1_ENST00000537824.1_Silent_p.P1943P|CSMD1_ENST00000400186.3_Silent_p.P1944P|CSMD1_ENST00000542608.1_Silent_p.P1943P|CSMD1_ENST00000539096.1_Silent_p.P1943P|CSMD1_ENST00000602557.1_Silent_p.P1944P|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Silent_p.P1944P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1944	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGGTGTACCCGGGCTCGCACT	0.517													G|||	11	0.00219649	0.0053	0.0	5008	,	,		16675	0.002		0.002	False		,,,				2504	0.0				p.P1943P		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C5829T						PASS	.	G		8,3932		0,8,1962	71.0	75.0	73.0		5829	-10.8	0.0	8	dbSNP_134	73	12,8308		0,12,4148	no	coding-synonymous	CSMD1	NM_033225.5		0,20,6110	AA,AG,GG		0.1442,0.203,0.1631		1943/3565	3019696	20,12240	1970	4160	6130	SO:0001819	synonymous_variant	64478	exon38			GTACCCGGGCTCG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5832C>T	8.37:g.3019696G>A		40.0	0.0	0		45.0	18.0	0.4	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	0.119	-1.128140	0.01770	0.00203	0.001442	ENSG00000183117	ENST00000335551	.	.	.	5.38	-10.8	0.00216	.	.	.	.	.	T	0.33731	0.0873	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	4	.	.	.	.	2.5509	0.04749	0.3963:0.2923:0.0797:0.2317	.	.	.	.	W	1424	.	.	R	-	1	2	CSMD1	3007103	0.000000	0.05858	0.005000	0.12908	0.154000	0.21943	-4.988000	0.00162	-5.089000	0.00022	-2.954000	0.00084	CGG	G|0.999;A|0.001	0.001	strong		0.517	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
BIRC6	57448	hgsc.bcm.edu	37	2	32774473	32774473	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:32774473C>T	ENST00000421745.2	+	65	13203	c.13069C>T	c.(13069-13071)Cct>Tct	p.P4357S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4357					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TAATGCCCTTCCTTCTGTACT	0.438																																					p.P4357S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C13069T						PASS	.						165.0	148.0	154.0					2																	32774473		2203	4300	6503	SO:0001583	missense	57448	exon65			GCCCTTCCTTCTG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13069C>T	2.37:g.32774473C>T	ENSP00000393596:p.Pro4357Ser	237.0	0.0	0		258.0	72.0	0.27907	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	16.37	3.105423	0.56291	.	.	ENSG00000115760	ENST00000421745	T	0.75821	-0.97	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.84986	0.5594	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85486	0.1182	10	0.72032	D	0.01	.	19.7806	0.96414	0.0:1.0:0.0:0.0	.	4357	Q9NR09	BIRC6_HUMAN	S	4357	ENSP00000393596:P4357S	ENSP00000393596:P4357S	P	+	1	0	BIRC6	32627977	1.000000	0.71417	0.982000	0.44146	0.060000	0.15804	7.818000	0.86416	2.669000	0.90835	0.650000	0.86243	CCT	.	.	none		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
CCDC54	84692	hgsc.bcm.edu	37	3	107096926	107096926	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:107096926A>C	ENST00000261058.1	+	1	739	c.492A>C	c.(490-492)aaA>aaC	p.K164N		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	164										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						AAAGGGGTAAAGAAATCACAG	0.418																																					p.K164N		Atlas-SNP	.											.	CCDC54	56	.	0			c.A492C						PASS	.						77.0	68.0	71.0					3																	107096926		2203	4300	6503	SO:0001583	missense	84692	exon1			GGGTAAAGAAATC	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.492A>C	3.37:g.107096926A>C	ENSP00000261058:p.Lys164Asn	207.0	0.0	0		215.0	50.0	0.232558	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	37	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	A	6.335	0.429836	0.11987	.	.	ENSG00000138483	ENST00000261058	T	0.55930	0.49	5.23	2.88	0.33553	.	0.487140	0.18842	N	0.129644	T	0.48960	0.1529	M	0.62723	1.935	0.09310	N	1	B	0.32051	0.354	B	0.37047	0.24	T	0.49351	-0.8949	10	0.66056	D	0.02	-0.8298	6.0356	0.19706	0.7984:0.0:0.2016:0.0	.	164	Q8NEL0	CCD54_HUMAN	N	164	ENSP00000261058:K164N	ENSP00000261058:K164N	K	+	3	2	CCDC54	108579616	0.978000	0.34361	0.080000	0.20451	0.012000	0.07955	2.718000	0.47236	0.841000	0.35020	0.377000	0.23210	AAA	.	.	none		0.418	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600	
SMTNL1	219537	hgsc.bcm.edu	37	11	57317522	57317522	+	Silent	SNP	A	A	G	rs117673759	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57317522A>G	ENST00000399154.2	+	8	1311	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	SMTNL1_ENST00000457912.1_Silent_p.T492T|SMTNL1_ENST00000527972.1_Silent_p.T474T			A8MU46	SMTL1_HUMAN	smoothelin-like 1	437	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						GCGTCTACACATACATCCAGG	0.557													A|||	4	0.000798722	0.0	0.0	5008	,	,		20156	0.0		0.004	False		,,,				2504	0.0				p.T474T		Atlas-SNP	.											.	SMTNL1	68	.	0			c.A1422G						PASS	.	A		8,4252		0,8,2122	69.0	71.0	70.0		1422	2.0	1.0	11	dbSNP_132	70	30,8438		0,30,4204	no	coding-synonymous	SMTNL1	NM_001105565.2		0,38,6326	GG,GA,AA		0.3543,0.1878,0.2986		474/495	57317522	38,12690	2130	4234	6364	SO:0001819	synonymous_variant	219537	exon7			CTACACATACATC	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"""calponin homology-associated smooth muscle protein"""	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.1311A>G	11.37:g.57317522A>G		115.0	0.0	0		112.0	50.0	0.446429	NM_001105565		Silent	SNP	ENST00000399154.2	37																																																																																				A|0.999;G|0.001	0.001	strong		0.557	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203	
CTAGE5	4253	hgsc.bcm.edu	37	14	39790149	39790149	+	Missense_Mutation	SNP	C	C	G	rs36060072	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39790149C>G	ENST00000280083.3	+	19	1875	c.1561C>G	c.(1561-1563)Ccc>Gcc	p.P521A	CTAGE5_ENST00000396158.2_Missense_Mutation_p.P526A|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.P1056A|CTAGE5_ENST00000341502.5_Missense_Mutation_p.P521A|CTAGE5_ENST00000341749.3_Missense_Mutation_p.P509A|CTAGE5_ENST00000396165.4_Missense_Mutation_p.P492A|CTAGE5_ENST00000553352.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000557038.1_Missense_Mutation_p.P441A|CTAGE5_ENST00000556148.1_Missense_Mutation_p.P446A|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000348007.3_Intron			O15320	CTGE5_HUMAN	CTAGE family, member 5	521	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		CCCATATGGTCCCTCACCATT	0.433													C|||	7	0.00139776	0.0	0.0	5008	,	,		16160	0.0		0.007	False		,,,				2504	0.0				p.P526A		Atlas-SNP	.											.	CTAGE5	75	.	0			c.C1576G						PASS	.	C	ALA/PRO,ALA/PRO,,ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	130.0	135.0	133.0		1561,1525,,1474	5.1	1.0	14	dbSNP_126	133	59,8541	35.3+/-89.8	0,59,4241	yes	missense,missense,intron,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	27,27,,27	0,61,6442	GG,GC,CC		0.686,0.0454,0.469	possibly-damaging,possibly-damaging,,possibly-damaging	521/805,509/793,,492/776	39790149	61,12945	2203	4300	6503	SO:0001583	missense	4253	exon19			TATGGTCCCTCAC	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1561C>G	14.37:g.39790149C>G	ENSP00000280083:p.Pro521Ala	86.0	0.0	0		100.0	52.0	0.52	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	19.63	3.864475	0.71949	4.54E-4	0.00686	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000553352	T;T;T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.95	5.06	0.68205	.	0.494861	0.15184	N	0.275926	T	0.70500	0.3231	M	0.88842	2.985	0.50467	D	0.999875	P;P;P;P	0.50528	0.936;0.936;0.936;0.936	P;P;P;P	0.56127	0.792;0.792;0.792;0.792	T	0.77619	-0.2520	9	.	.	.	.	15.5102	0.75776	0.0:0.8624:0.1376:0.0	rs36060072	483;526;521;509	F8W9E1;O15320-5;O15320;G3XAC5	.;.;CTGE5_HUMAN;.	A	1056;509;441;483;492;521;526;521;446;492	ENSP00000452252:P1056A;ENSP00000343897:P509A;ENSP00000450869:P441A;ENSP00000379468:P492A;ENSP00000339286:P521A;ENSP00000379462:P526A;ENSP00000280083:P521A;ENSP00000452562:P446A;ENSP00000450449:P492A	.	P	+	1	0	CTAGE5;RP11-407N17.3	38859900	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.350000	0.59392	1.503000	0.48686	0.655000	0.94253	CCC	G|0.005;C|0.995	0.005	strong		0.433	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
ZBBX	79740	hgsc.bcm.edu	37	3	167023485	167023485	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167023485G>T	ENST00000392766.2	-	17	2011	c.1671C>A	c.(1669-1671)agC>agA	p.S557R	ZBBX_ENST00000307529.5_Missense_Mutation_p.S557R|ZBBX_ENST00000455345.2_Missense_Mutation_p.S557R|ZBBX_ENST00000392767.2_Missense_Mutation_p.S557R|ZBBX_ENST00000392764.1_Missense_Mutation_p.S528R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	557						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TATACAGATTGCTCAATTCCA	0.318																																					p.S557R		Atlas-SNP	.											.	ZBBX	299	.	0			c.C1671A						PASS	.						73.0	65.0	67.0					3																	167023485		1805	4064	5869	SO:0001583	missense	79740	exon17			CAGATTGCTCAAT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1671C>A	3.37:g.167023485G>T	ENSP00000376519:p.Ser557Arg	202.0	0.0	0		169.0	37.0	0.218935	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	G	9.950	1.219989	0.22373	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.12672	2.83;2.83;2.84;2.84;2.66	5.3	0.467	0.16721	.	0.470940	0.24740	N	0.035987	T	0.17959	0.0431	L	0.59436	1.845	0.09310	N	1	D;D	0.59357	0.985;0.975	P;P	0.52217	0.693;0.497	T	0.07139	-1.0788	10	0.66056	D	0.02	-1.3445	4.9275	0.13901	0.344:0.1509:0.5051:0.0	.	557;557	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	557;557;557;557;528	ENSP00000376519:S557R;ENSP00000376520:S557R;ENSP00000390232:S557R;ENSP00000305065:S557R;ENSP00000376517:S528R	ENSP00000305065:S557R	S	-	3	2	ZBBX	168506179	0.266000	0.24112	0.013000	0.15412	0.012000	0.07955	-0.013000	0.12678	0.142000	0.18901	0.650000	0.86243	AGC	.	.	none		0.318	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751891	140751891	+	Missense_Mutation	SNP	G	G	A	rs559633972		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140751891G>A	ENST00000576222.1	+	1	2061	c.1930G>A	c.(1930-1932)Gtc>Atc	p.V644I	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	644	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCTGCTGGTCACTGTGCG	0.647													.|||	1	0.000199681	0.0	0.0	5008	,	,		18457	0.001		0.0	False		,,,				2504	0.0				p.V644I		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.G1930A						PASS	.						44.0	49.0	48.0					5																	140751891		2110	4238	6348	SO:0001583	missense	56102	exon1			CTGCTGGTCACTG	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1930G>A	5.37:g.140751891G>A	ENSP00000461862:p.Val644Ile	35.0	0.0	0		27.0	9.0	0.333333	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			.	.	none		0.647	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
PRR22	163154	hgsc.bcm.edu	37	19	5783840	5783840	+	Missense_Mutation	SNP	G	G	C	rs576156353	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5783840G>C	ENST00000419421.2	-	3	522	c.418C>G	c.(418-420)Ccc>Gcc	p.P140A		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	140	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						AGAAACTGGGGCCCCCCGGGT	0.716													G|||	2	0.000399361	0.0	0.0	5008	,	,		10475	0.0		0.001	False		,,,				2504	0.001				p.P140A		Atlas-SNP	.											.	PRR22	25	.	0			c.C418G						PASS	.																																			SO:0001583	missense	163154	exon3			ACTGGGGCCCCCC	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.418C>G	19.37:g.5783840G>C	ENSP00000407653:p.Pro140Ala	19.0	0.0	0		36.0	14.0	0.388889	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329912	0.24167	.	.	ENSG00000212123	ENST00000419421	T	0.50277	0.75	4.55	3.49	0.39957	.	.	.	.	.	T	0.37919	0.1021	L	0.32530	0.975	0.27285	N	0.957999	P;P	0.40332	0.713;0.713	B;B	0.37304	0.162;0.246	T	0.26224	-1.0109	9	0.87932	D	0	-5.6709	12.2151	0.54402	0.0:0.1737:0.8263:0.0	.	140;138	E9PB31;Q8IZ63	.;PRR22_HUMAN	A	140	ENSP00000407653:P140A	ENSP00000407653:P140A	P	-	1	0	PRR22	5734840	0.003000	0.15002	0.252000	0.24328	0.010000	0.07245	0.703000	0.25646	1.096000	0.41439	-0.479000	0.04858	CCC	.	.	none		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
TANK	10010	hgsc.bcm.edu	37	2	162036195	162036195	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:162036195C>T	ENST00000392749.2	+	2	261	c.22C>T	c.(22-24)Caa>Taa	p.Q8*	TANK_ENST00000406287.1_Nonsense_Mutation_p.Q66*|TANK_ENST00000402568.1_Nonsense_Mutation_p.Q66*|TANK_ENST00000405852.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000457476.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000259075.2_Nonsense_Mutation_p.Q8*|TANK_ENST00000403609.1_Nonsense_Mutation_p.Q8*	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	8					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CATTGGCGAGCAACTCAATAA	0.393																																					p.Q8X		Atlas-SNP	.											.	TANK	35	.	0			c.C22T						PASS	.						123.0	113.0	117.0					2																	162036195		2203	4300	6503	SO:0001587	stop_gained	10010	exon2			GGCGAGCAACTCA	U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.22C>T	2.37:g.162036195C>T	ENSP00000376505:p.Gln8*	136.0	0.0	0		100.0	41.0	0.41	NM_004180	D3DPB5|Q7Z4J6|Q92885	Nonsense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.	.	.	.	.	.	.	.	.	.	C	38	6.652831	0.97734	.	.	ENSG00000136560	ENST00000259075;ENST00000432002;ENST00000457476;ENST00000392749;ENST00000440506;ENST00000429217;ENST00000406287;ENST00000402568;ENST00000405852;ENST00000456358;ENST00000403609	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-11.5692	20.1743	0.98175	0.0:1.0:0.0:0.0	.	.	.	.	X	8;8;8;8;8;8;66;66;8;34;8	.	ENSP00000259075:Q8X	Q	+	1	0	TANK	161744441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.913000	0.69957	2.873000	0.98535	0.561000	0.74099	CAA	.	.	none		0.393	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484	
LAMA2	3908	hgsc.bcm.edu	37	6	129813567	129813567	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:129813567T>A	ENST00000421865.2	+	58	8232	c.8183T>A	c.(8182-8184)gTt>gAt	p.V2728D	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2728					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCTGAAATAGTTATCCAGCCT	0.473																																					p.V2728D		Atlas-SNP	.											.	LAMA2	481	.	0			c.T8183A						PASS	.						92.0	95.0	94.0					6																	129813567		2203	4300	6503	SO:0001583	missense	3908	exon58			AAATAGTTATCCA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8183T>A	6.37:g.129813567T>A	ENSP00000400365:p.Val2728Asp	90.0	0.0	0		73.0	39.0	0.534247	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.031933	0.35893	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.34072	1.38	5.62	4.43	0.53597	.	0.789321	0.11925	N	0.516246	T	0.08802	0.0218	N	0.22421	0.69	0.09310	N	0.999995	B;B	0.28552	0.215;0.121	B;B	0.26517	0.07;0.051	T	0.29336	-1.0015	9	.	.	.	.	6.9619	0.24601	0.1322:0.071:0.0:0.7969	.	2729;2728	A6NF00;P24043	.;LAMA2_HUMAN	D	2728;2727;2728;746	ENSP00000400365:V2728D	.	V	+	2	0	LAMA2	129855260	0.038000	0.19896	0.001000	0.08648	0.077000	0.17291	2.630000	0.46494	0.921000	0.36994	0.460000	0.39030	GTT	.	.	none		0.473	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ENGASE	64772	hgsc.bcm.edu	37	17	77075631	77075631	+	Silent	SNP	C	C	T	rs3744182	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77075631C>T	ENST00000579016.1	+	4	477	c.477C>T	c.(475-477)gaC>gaT	p.D159D	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	159						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						AGTGCATCGACGTCTTTGTGT	0.587													C|||	721	0.14397	0.3865	0.0893	5008	,	,		19787	0.0476		0.0427	False		,,,				2504	0.0583				p.D159D		Atlas-SNP	.											ENGASE,NS,carcinoma,+2,2	ENGASE	55	2	0			c.C477T						PASS	.	C		1255,2959		185,885,1037	134.0	156.0	149.0		477	5.2	1.0	17	dbSNP_107	149	329,8093		3,323,3885	no	coding-synonymous	ENGASE	NM_001042573.1		188,1208,4922	TT,TC,CC		3.9064,29.7817,12.5356		159/744	77075631	1584,11052	2107	4211	6318	SO:0001819	synonymous_variant	64772	exon4			CATCGACGTCTTT	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.477C>T	17.37:g.77075631C>T		84.0	0.0	0		72.0	23.0	0.319444	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			C|0.878;T|0.122	0.122	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
HUNK	30811	hgsc.bcm.edu	37	21	33368191	33368191	+	Missense_Mutation	SNP	G	G	C	rs138721520	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33368191G>C	ENST00000270112.2	+	10	1776	c.1416G>C	c.(1414-1416)atG>atC	p.M472I	HUNK_ENST00000465574.1_3'UTR	NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	472					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						GCTCGCTTATGACACAGATTC	0.532													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.M472I		Atlas-SNP	.											.	HUNK	74	.	0			c.G1416C						PASS	.	G	ILE/MET	34,4372	39.2+/-71.8	0,34,2169	57.0	54.0	55.0		1416	0.3	0.0	21	dbSNP_134	55	0,8600		0,0,4300	yes	missense	HUNK	NM_014586.1	10	0,34,6469	CC,CG,GG		0.0,0.7717,0.2614	benign	472/715	33368191	34,12972	2203	4300	6503	SO:0001583	missense	30811	exon10			GCTTATGACACAG	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1416G>C	21.37:g.33368191G>C	ENSP00000270112:p.Met472Ile	162.0	0.0	0		180.0	106.0	0.588889	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.003	-2.395865	0.00198	0.007717	0.0	ENSG00000142149	ENST00000270112;ENST00000439107	T	0.63417	-0.04	4.34	0.337	0.15966	.	0.591295	0.16443	N	0.214240	T	0.22126	0.0533	N	0.01576	-0.805	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.18023	-1.0350	10	0.25751	T	0.34	-4.655	9.205	0.37285	0.0:0.4763:0.443:0.0807	.	472	P57058	HUNK_HUMAN	I	472;86	ENSP00000270112:M472I	ENSP00000270112:M472I	M	+	3	0	HUNK	32290062	0.393000	0.25237	0.004000	0.12327	0.031000	0.12232	0.727000	0.25999	-0.133000	0.11537	-0.867000	0.03001	ATG	G|0.998;C|0.002	0.002	strong		0.532	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
HAGHL	84264	hgsc.bcm.edu	37	16	777590	777590	+	Silent	SNP	C	C	T	rs143758903	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:777590C>T	ENST00000341413.4	+	2	362	c.81C>T	c.(79-81)gcC>gcT	p.A27A	HAGHL_ENST00000549114.1_Silent_p.A27A|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000389703.3_Silent_p.A27A|HAGHL_ENST00000564545.1_Silent_p.A27A|HAGHL_ENST00000561546.1_Silent_p.A27A|HAGHL_ENST00000564537.1_Silent_p.A27A|CCDC78_ENST00000293889.6_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	27							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				AGGCGGTGGCCGTGGACGTGG	0.697													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11895	0.0		0.002	False		,,,				2504	0.0				p.A27A	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.C81T						PASS	.	C		0,4374		0,0,2187	53.0	39.0	44.0		81	-5.0	0.0	16	dbSNP_134	44	19,8569	12.6+/-44.7	0,19,4275	no	coding-synonymous	HAGHL	NM_032304.2		0,19,6462	TT,TC,CC		0.2212,0.0,0.1466		27/283	777590	19,12943	2187	4294	6481	SO:0001819	synonymous_variant	84264	exon1			GGTGGCCGTGGAC	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.81C>T	16.37:g.777590C>T		92.0	0.0	0		96.0	45.0	0.46875	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				C|0.999;T|0.001	0.001	strong		0.697	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
CD48	962	hgsc.bcm.edu	37	1	160681535	160681535	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160681535C>T	ENST00000368046.3	-	1	106	c.19G>A	c.(19-21)Gat>Aat	p.D7N	CD48_ENST00000368045.3_Missense_Mutation_p.D7N	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	7					blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			AGACACGAATCCCAACCTCTG	0.512																																					p.D7N		Atlas-SNP	.											.	CD48	31	.	0			c.G19A						PASS	.						116.0	94.0	102.0					1																	160681535		2203	4300	6503	SO:0001583	missense	962	exon1			ACGAATCCCAACC	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.19G>A	1.37:g.160681535C>T	ENSP00000357025:p.Asp7Asn	275.0	0.0	0		265.0	53.0	0.2	NM_001256030	Q5U055|Q8MGR0	Missense_Mutation	SNP	ENST00000368046.3	37	CCDS1208.1	.	.	.	.	.	.	.	.	.	.	C	3.053	-0.194989	0.06259	.	.	ENSG00000117091	ENST00000368046;ENST00000368045	T;T	0.50001	3.91;0.76	4.06	-8.12	0.01078	.	4.906520	0.00166	N	0.000004	T	0.06050	0.0157	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.05699	-1.0869	10	0.30854	T	0.27	-16.7883	5.9139	0.19043	0.0895:0.2615:0.0886:0.5604	.	7;7;7	Q8MGR0;Q6IAZ2;P09326	.;.;CD48_HUMAN	N	7	ENSP00000357025:D7N;ENSP00000357024:D7N	ENSP00000357024:D7N	D	-	1	0	CD48	158948159	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.228000	0.01209	-3.054000	0.00259	-2.852000	0.00102	GAT	.	.	none		0.512	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
PAX5	5079	hgsc.bcm.edu	37	9	37033992	37033992	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:37033992T>C	ENST00000358127.4	-	1	111	c.37A>G	c.(37-39)Agc>Ggc	p.S13G	PAX5_ENST00000520281.1_Missense_Mutation_p.S13G|PAX5_ENST00000523241.1_Missense_Mutation_p.S13G|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000377847.2_Missense_Mutation_p.S13G|PAX5_ENST00000520154.1_Missense_Mutation_p.S13G|PAX5_ENST00000414447.1_Missense_Mutation_p.S13G|PAX5_ENST00000446742.1_Missense_Mutation_p.S13G|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000377853.2_Missense_Mutation_p.S13G|PAX5_ENST00000377852.2_Missense_Mutation_p.S13G	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	13					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(10)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		CCTGTCCTGCTGGTCCGAGGA	0.522			"""T, Mis, D, F, S"""	"""IGH@, ETV6, PML, FOXP1, ZNF521, ELN"""	"""NHL, ALL, B-ALL"""																																p.S13G		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	10	Unknown(10)	haematopoietic_and_lymphoid_tissue(10)	c.A37G						PASS	.						67.0	63.0	64.0					9																	37033992		2203	4300	6503	SO:0001583	missense	5079	exon1			TCCTGCTGGTCCG		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"""Paired boxes"", ""Homeoboxes / PRD class"""	8619	protein-coding gene	gene with protein product	"""B-cell lineage specific activator"""	167414	"""paired box gene 5 (B-cell lineage specific activator protein)"", ""paired box gene 5 (B-cell lineage specific activator)"""			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.37A>G	9.37:g.37033992T>C	ENSP00000350844:p.Ser13Gly	61.0	0.0	0		89.0	41.0	0.460674	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.276510	0.40294	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.97924	-4.13;-4.13;-4.12;-4.61;-4.61;-4.54;-3.77;-4.54;-4.61	6.08	0.879	0.19155	.	0.627134	0.17080	N	0.187840	D	0.92133	0.7506	N	0.16862	0.45	0.27406	N	0.954724	B;B;B;B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.001;0.002;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.08055	0.0;0.0;0.0;0.0;0.003;0.001;0.0;0.0;0.0	D	0.84947	0.0869	10	0.42905	T	0.14	.	5.7732	0.18265	0.1214:0.5281:0.0:0.3505	.	13;13;13;13;13;13;13;13;13	C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;PAX5_HUMAN	G	13	ENSP00000350844:S13G;ENSP00000367084:S13G;ENSP00000367083:S13G;ENSP00000429637:S13G;ENSP00000429291:S13G;ENSP00000430773:S13G;ENSP00000404687:S13G;ENSP00000412188:S13G;ENSP00000367078:S13G	ENSP00000350844:S13G	S	-	1	0	PAX5	37023992	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	1.043000	0.30316	-0.099000	0.12263	0.533000	0.62120	AGC	.	.	none		0.522	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		
PRR30	339779	hgsc.bcm.edu	37	2	27360773	27360773	+	Missense_Mutation	SNP	G	G	A	rs61741796	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27360773G>A	ENST00000335524.3	-	3	950	c.425C>T	c.(424-426)cCt>cTt	p.P142L		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		142	Pro-rich.									cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ggactggcaaggtgagtgggg	0.612													g|||	11	0.00219649	0.0	0.0014	5008	,	,		15255	0.0		0.0089	False		,,,				2504	0.001				p.P142L		Atlas-SNP	.											.	C2orf53	45	.	0			c.C425T						PASS	.		LEU/PRO	13,4393	17.9+/-39.9	0,13,2190	37.0	39.0	38.0		425	-9.5	0.0	2	dbSNP_129	38	92,8508	49.8+/-109.6	0,92,4208	yes	missense	C2orf53	NM_178553.3	98	0,105,6398	AA,AG,GG		1.0698,0.2951,0.8073	benign	142/413	27360773	105,12901	2203	4300	6503	SO:0001583	missense	339779	exon3			TGGCAAGGTGAGT																												ENST00000335524.3:c.425C>T	2.37:g.27360773G>A	ENSP00000335017:p.Pro142Leu	47.0	0.0	0		43.0	20.0	0.465116	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	g	8.874	0.949947	0.18431	0.002951	0.010698	ENSG00000186143	ENST00000335524	T	0.30182	1.54	4.75	-9.51	0.00581	.	2.854260	0.01695	N	0.026858	T	0.10852	0.0265	N	0.14661	0.345	0.09310	N	1	B	0.29037	0.231	B	0.25405	0.06	T	0.08700	-1.0709	10	0.36615	T	0.2	3.6732	8.0189	0.30398	0.0677:0.1111:0.5291:0.2922	.	142	Q53SZ7	CB053_HUMAN	L	142	ENSP00000335017:P142L	ENSP00000335017:P142L	P	-	2	0	C2orf53	27214277	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.954000	0.00676	-2.979000	0.00283	-0.271000	0.10264	CCT	G|0.993;A|0.007	0.007	strong		0.612	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1		
RFTN2	130132	hgsc.bcm.edu	37	2	198498595	198498595	+	Missense_Mutation	SNP	C	C	T	rs139323535	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:198498595C>T	ENST00000295049.4	-	4	1101	c.565G>A	c.(565-567)Ggt>Agt	p.G189S		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	189					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)		p.G189S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TCATCTGAACCGTGTCTCACA	0.398													C|||	7	0.00139776	0.0008	0.0014	5008	,	,		18759	0.0		0.003	False		,,,				2504	0.002				p.G189S		Atlas-SNP	.											RFTN2,NS,carcinoma,0,2	RFTN2	68	2	1	Substitution - Missense(1)	endometrium(1)	c.G565A						PASS	.	C	SER/GLY	2,4404	4.2+/-10.8	0,2,2201	226.0	203.0	211.0		565	-5.2	0.0	2	dbSNP_134	211	26,8574	20.4+/-63.3	0,26,4274	yes	missense	RFTN2	NM_144629.2	56	0,28,6475	TT,TC,CC		0.3023,0.0454,0.2153	benign	189/502	198498595	28,12978	2203	4300	6503	SO:0001583	missense	130132	exon4			CTGAACCGTGTCT	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 11"""	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.565G>A	2.37:g.198498595C>T	ENSP00000295049:p.Gly189Ser	173.0	0.0	0		170.0	85.0	0.5	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	37	CCDS2323.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	7.139	0.581532	0.13686	4.54E-4	0.003023	ENSG00000162944	ENST00000295049	T	0.28255	1.62	5.22	-5.18	0.02840	.	1.217120	0.05880	N	0.626229	T	0.10680	0.0261	N	0.03000	-0.44	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30090	-0.9990	10	0.16420	T	0.52	0.237	6.8081	0.23788	0.1139:0.398:0.0:0.4881	.	189	Q52LD8	RFTN2_HUMAN	S	189	ENSP00000295049:G189S	ENSP00000295049:G189S	G	-	1	0	RFTN2	198206840	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.341000	0.07811	-1.232000	0.02554	-1.099000	0.02127	GGT	C|0.998;T|0.002	0.002	strong		0.398	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629	
MCMDC2	157777	hgsc.bcm.edu	37	8	67786817	67786817	+	Missense_Mutation	SNP	C	C	T	rs116671744	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67786817C>T	ENST00000422365.2	+	4	452	c.281C>T	c.(280-282)aCg>aTg	p.T94M	MCMDC2_ENST00000541540.1_Missense_Mutation_p.T31M|MCMDC2_ENST00000469823.1_3'UTR|MCMDC2_ENST00000313616.5_Missense_Mutation_p.T94M|MCMDC2_ENST00000396592.3_Missense_Mutation_p.T94M|MCMDC2_ENST00000492775.1_Missense_Mutation_p.T94M	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	94				T -> M (in Ref. 1; BAG63905). {ECO:0000305}.	DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						CAGACTGAAACGCAAGTAAGT	0.289													C|||	188	0.0375399	0.0469	0.0576	5008	,	,		14741	0.0079		0.0288	False		,,,				2504	0.0501				p.T94M		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C281T						PASS	.	C	MET/THR,MET/THR,MET/THR	170,4234	109.9+/-148.2	1,168,2033	70.0	63.0	65.0		281,281,281	2.0	1.0	8	dbSNP_132	65	271,8323	102.3+/-163.5	4,263,4030	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	81,81,81	5,431,6063	TT,TC,CC		3.1534,3.8601,3.3928	probably-damaging,probably-damaging,probably-damaging	94/633,94/591,94/682	67786817	441,12557	2202	4297	6499	SO:0001583	missense	157777	exon4			CTGAAACGCAAGT	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.281C>T	8.37:g.67786817C>T	ENSP00000413632:p.Thr94Met	120.0	0.0	0		117.0	50.0	0.42735	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	69	0.03159340659340659	18	0.036585365853658534	18	0.049723756906077346	6	0.01048951048951049	27	0.03562005277044855	C	12.79	2.043193	0.36085	0.038601	0.031534	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616;ENST00000541540	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	4.87	2.04	0.26737	.	0.229019	0.45361	D	0.000376	T	0.03739	0.0106	L	0.44542	1.39	0.27205	N	0.960063	B;B;B;B	0.18610	0.029;0.017;0.017;0.029	B;B;B;B	0.13407	0.009;0.004;0.004;0.009	T	0.08207	-1.0733	10	0.41790	T	0.15	-2.164	8.4645	0.32947	0.3907:0.5391:0.0:0.0702	.	31;94;94;94	Q4G0Z9-4;Q4G0Z9;B4DXX4;G3XAN3	.;CH045_HUMAN;.;.	M	94;94;94;94;31	ENSP00000379837:T94M;ENSP00000413632:T94M;ENSP00000428037:T94M;ENSP00000317234:T94M;ENSP00000445629:T31M	ENSP00000317234:T94M	T	+	2	0	C8orf45	67949371	0.790000	0.28787	0.965000	0.40720	0.533000	0.34776	0.902000	0.28459	0.194000	0.20326	-0.142000	0.14014	ACG	C|0.970;T|0.030	0.030	strong		0.289	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
TOX3	27324	hgsc.bcm.edu	37	16	52484278	52484278	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:52484278G>A	ENST00000219746.9	-	4	873	c.589C>T	c.(589-591)Cac>Tac	p.H197Y	TOX3_ENST00000407228.3_Missense_Mutation_p.H192Y	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	197					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GGAGATGTGTGAGGCATACTG	0.547																																					p.H197Y		Atlas-SNP	.											.	TOX3	121	.	0			c.C589T						PASS	.						147.0	152.0	150.0					16																	52484278		2125	4226	6351	SO:0001583	missense	27324	exon4			ATGTGTGAGGCAT	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.589C>T	16.37:g.52484278G>A	ENSP00000219746:p.His197Tyr	97.0	0.0	0		113.0	33.0	0.292035	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234074	0.58886	.	.	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.12569	2.68;2.67	5.71	3.66	0.41972	.	0.106561	0.64402	D	0.000006	T	0.18841	0.0452	M	0.73962	2.25	0.54753	D	0.999981	B;B	0.14438	0.01;0.01	B;B	0.11329	0.004;0.006	T	0.04320	-1.0960	10	0.52906	T	0.07	.	12.9391	0.58333	0.0:0.1241:0.7467:0.1292	.	192;197	B4DRD0;O15405	.;TOX3_HUMAN	Y	197;192	ENSP00000219746:H197Y;ENSP00000385705:H192Y	ENSP00000219746:H197Y	H	-	1	0	TOX3	51041779	1.000000	0.71417	1.000000	0.80357	0.399000	0.30720	8.052000	0.89448	1.388000	0.46506	-0.309000	0.09137	CAC	.	.	none		0.547	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
SYMPK	8189	hgsc.bcm.edu	37	19	46320218	46320218	+	Silent	SNP	G	G	A	rs140350780		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46320218G>A	ENST00000245934.7	-	24	3340	c.3096C>T	c.(3094-3096)ccC>ccT	p.P1032P	RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1032					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CCCACACCTTGGGGTACTTCC	0.632											OREG0025562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		15216	0.0		0.001	False		,,,				2504	0.0				p.P1032P		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3096T						PASS	.	G		1,4385		0,1,2192	24.0	22.0	23.0		3096	4.7	1.0	19	dbSNP_134	23	38,8512		0,38,4237	no	coding-synonymous	SYMPK	NM_004819.2		0,39,6429	AA,AG,GG		0.4444,0.0228,0.3015		1032/1275	46320218	39,12897	2193	4275	6468	SO:0001819	synonymous_variant	8189	exon24			CACCTTGGGGTAC	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3096C>T	19.37:g.46320218G>A		110.0	0.0	0	938	92.0	47.0	0.51087	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			G|0.997;A|0.003	0.003	strong		0.632	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
ATAD3B	83858	hgsc.bcm.edu	37	1	1425644	1425644	+	Missense_Mutation	SNP	C	C	G	rs373123252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1425644C>G	ENST00000308647.7	+	14	1461	c.1345C>G	c.(1345-1347)Ctg>Gtg	p.L449V		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	449						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CAGATTCATGCTGGTCCTGGC	0.627																																					p.L449V		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1345G						PASS	.	C	VAL/LEU	0,4402		0,0,2201	62.0	59.0	60.0		1345	2.1	1.0	1		60	2,8596		0,2,4297	no	missense	ATAD3B	NM_031921.4	32	0,2,6498	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging	449/649	1425644	2,12998	2201	4299	6500	SO:0001583	missense	83858	exon14			TTCATGCTGGTCC	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1345C>G	1.37:g.1425644C>G	ENSP00000311766:p.Leu449Val	92.0	0.0	0		101.0	50.0	0.49505	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	10.95	1.495279	0.26774	0.0	2.33E-4	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.94497	-3.44	2.07	2.07	0.26955	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000001	D	0.91250	0.7242	N	0.10782	0.045	0.80722	D	1	D;P	0.54397	0.966;0.946	P;P	0.58130	0.833;0.822	D	0.90536	0.4499	10	0.49607	T	0.09	.	11.3902	0.49809	0.0:1.0:0.0:0.0	.	403;449	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	V	252;449	ENSP00000311766:L449V	ENSP00000311766:L449V	L	+	1	2	ATAD3B	1415507	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	2.740000	0.47418	1.139000	0.42245	0.205000	0.17691	CTG	.	.	none		0.627	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
KHDRBS1	10657	hgsc.bcm.edu	37	1	32479924	32479924	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32479924G>A	ENST00000327300.7	+	1	495	c.328G>A	c.(328-330)Gag>Aag	p.E110K	KHDRBS1_ENST00000492989.1_Missense_Mutation_p.E110K|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1											endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ACTCATGGCCGAGAAGGACTC	0.692																																					p.E110K	Ovarian(173;401 1982 12359 31110 42403)	Atlas-SNP	.											.	KHDRBS1	34	.	0			c.G328A						PASS	.						22.0	19.0	20.0					1																	32479924		2199	4294	6493	SO:0001583	missense	10657	exon1			ATGGCCGAGAAGG	U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"""GAP-associated tyrosine phosphoprotein p62 (Sam68)"""	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.328G>A	1.37:g.32479924G>A	ENSP00000313829:p.Glu110Lys	73.0	0.0	0		84.0	28.0	0.333333	NM_006559		Missense_Mutation	SNP	ENST00000327300.7	37	CCDS350.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637903	0.87760	.	.	ENSG00000121774	ENST00000327300;ENST00000492989;ENST00000355201	T;T	0.61510	0.48;0.1	4.18	3.26	0.37387	.	0.101044	0.64402	D	0.000002	T	0.73313	0.3571	M	0.77820	2.39	0.58432	D	0.999995	D;D	0.89917	0.997;1.0	P;D	0.67382	0.842;0.951	T	0.77965	-0.2389	10	0.87932	D	0	.	12.9521	0.58407	0.0:0.1634:0.8365:0.0	.	110;110	Q07666;Q07666-3	KHDR1_HUMAN;.	K	110;110;86	ENSP00000313829:E110K;ENSP00000417731:E110K	ENSP00000313829:E110K	E	+	1	0	KHDRBS1	32252511	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	5.345000	0.65987	1.339000	0.45563	0.655000	0.94253	GAG	.	.	none		0.692	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559	
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77911745C>T	ENST00000529308.1	+	6	1349	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_Missense_Mutation_p.S94L|USP35_ENST00000530535.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			AAGGAGGACTCGAACTCGGGG	0.647													C|||	19	0.00379393	0.0015	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0082				p.S363L		Atlas-SNP	.											USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	0			c.C1088T						PASS	.	C	LEU/SER	5,3907		0,5,1951	46.0	52.0	50.0		1088	4.7	1.0	11	dbSNP_134	50	46,8202		0,46,4078	yes	missense	USP35	NM_020798.2	145	0,51,6029	TT,TC,CC		0.5577,0.1278,0.4194	benign	363/1019	77911745	51,12109	1956	4124	6080	SO:0001583	missense	57558	exon6			AGGACTCGAACTC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1088C>T	11.37:g.77911745C>T	ENSP00000431876:p.Ser363Leu	95.0	0.0	0		119.0	95.0	0.798319	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	13.79	2.343705	0.41498	0.001278	0.005577	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68181	-0.24;-0.31;3.37	4.73	4.73	0.59995	Armadillo-like helical (1);	0.000000	0.52532	D	0.000071	T	0.40448	0.1117	N	0.19112	0.55	0.80722	D	1	B	0.33739	0.422	B	0.22753	0.041	T	0.43925	-0.9361	10	0.18276	T	0.48	-15.0401	17.9135	0.88942	0.0:1.0:0.0:0.0	.	363	Q9P2H5	UBP35_HUMAN	L	119;363;94	ENSP00000436001:S119L;ENSP00000431876:S363L;ENSP00000434942:S94L	ENSP00000434942:S94L	S	+	2	0	USP35	77589393	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.484000	0.66844	2.461000	0.83175	0.561000	0.74099	TCG	C|0.996;T|0.004	0.004	strong		0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
SAMD9L	219285	hgsc.bcm.edu	37	7	92761064	92761064	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92761064T>G	ENST00000318238.4	-	5	5437	c.4221A>C	c.(4219-4221)aaA>aaC	p.K1407N	SAMD9L_ENST00000411955.1_Missense_Mutation_p.K1407N|SAMD9L_ENST00000437805.1_Missense_Mutation_p.K1407N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1407					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			GGAGTTGTTTTTTTAGCGTGG	0.413																																					p.K1407N		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A4221C						PASS	.						156.0	157.0	157.0					7																	92761064		2203	4300	6503	SO:0001583	missense	219285	exon5			TTGTTTTTTTAGC	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4221A>C	7.37:g.92761064T>G	ENSP00000326247:p.Lys1407Asn	63.0	0.0	0		75.0	17.0	0.226667	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	T	9.547	1.114998	0.20795	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.24350	1.86;1.86;1.86	5.22	1.58	0.23477	.	0.272209	0.30781	N	0.008884	T	0.36963	0.0986	L	0.47716	1.5	0.20307	N	0.999919	D	0.71674	0.998	D	0.66351	0.943	T	0.08617	-1.0713	10	0.62326	D	0.03	-22.1012	9.3808	0.38313	0.0:0.2436:0.0:0.7564	.	1407	Q8IVG5	SAM9L_HUMAN	N	1407;1407;1407;229	ENSP00000326247:K1407N;ENSP00000405760:K1407N;ENSP00000408796:K1407N	ENSP00000326247:K1407N	K	-	3	2	SAMD9L	92599000	0.000000	0.05858	0.971000	0.41717	0.037000	0.13140	0.116000	0.15561	0.458000	0.26988	0.383000	0.25322	AAA	.	.	none		0.413	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
OR10A5	144124	hgsc.bcm.edu	37	11	6867588	6867588	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6867588T>C	ENST00000299454.4	+	1	706	c.675T>C	c.(673-675)gcT>gcC	p.A225A	OR10A5_ENST00000379831.2_Silent_p.A229A			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	225					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTGCTGCTGCTATCCTCAAGA	0.473																																					p.A225A	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.T675C						PASS	.						286.0	234.0	252.0					11																	6867588		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			TGCTGCTATCCTC	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.675T>C	11.37:g.6867588T>C		243.0	0.0	0		224.0	12.0	0.0535714	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																			.	.	none		0.473	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744062	31744062	+	Missense_Mutation	SNP	C	C	A	rs150635388	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31744062C>A	ENST00000399889.2	-	1	495	c.470G>T	c.(469-471)tGc>tTc	p.C157F		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	157						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						AGGAGACTGGCAGCTCCTAGA	0.507													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18428	0.0		0.004	False		,,,				2504	0.0				p.C157F		Atlas-SNP	.											KRTAP13-2,NS,carcinoma,0,1	KRTAP13-2	29	1	0			c.G470T						PASS	.	C	PHE/CYS	1,4405	2.1+/-5.4	0,1,2202	72.0	67.0	69.0		470	-1.0	0.0	21	dbSNP_134	69	22,8578	16.0+/-53.3	0,22,4278	yes	missense	KRTAP13-2	NM_181621.3	205	0,23,6480	AA,AC,CC		0.2558,0.0227,0.1768	benign	157/176	31744062	23,12983	2203	4300	6503	SO:0001583	missense	337959	exon1			GACTGGCAGCTCC	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.470G>T	21.37:g.31744062C>A	ENSP00000382777:p.Cys157Phe	105.0	0.0	0		110.0	65.0	0.590909	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	0.070	-1.205164	0.01568	2.27E-4	0.002558	ENSG00000182816	ENST00000399889	T	0.02863	4.13	5.02	-0.986	0.10252	.	0.755961	0.11281	N	0.580344	T	0.01940	0.0061	N	0.17564	0.495	0.09310	N	1	B	0.13594	0.008	B	0.14023	0.01	T	0.48281	-0.9049	10	0.21540	T	0.41	.	8.3543	0.32321	0.4947:0.4264:0.0:0.0789	.	157	Q52LG2	KR132_HUMAN	F	157	ENSP00000382777:C157F	ENSP00000382777:C157F	C	-	2	0	KRTAP13-2	30665933	0.106000	0.21978	0.001000	0.08648	0.976000	0.68499	-0.467000	0.06664	-0.305000	0.08831	0.655000	0.94253	TGC	C|0.999;A|0.001	0.001	strong		0.507	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
KIAA0196	9897	hgsc.bcm.edu	37	8	126056088	126056088	+	Silent	SNP	C	C	T	rs369339497		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:126056088C>T	ENST00000318410.7	-	23	3178	c.2829G>A	c.(2827-2829)gcG>gcA	p.A943A	KIAA0196_ENST00000517845.1_Silent_p.A795A|KIAA0196-AS1_ENST00000519140.1_RNA	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	943					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			CCTCGAGATACGCAGTCCAAA	0.303													C|||	1	0.000199681	0.0	0.0	5008	,	,		17952	0.001		0.0	False		,,,				2504	0.0				p.A943A		Atlas-SNP	.											KIAA0196,NS,carcinoma,0,1	KIAA0196	90	1	0			c.G2829A						PASS	.	C		0,4406		0,0,2203	84.0	78.0	80.0		2829	-0.0	0.9	8		80	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		943/1160	126056088	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon23			GAGATACGCAGTC		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2829G>A	8.37:g.126056088C>T		112.0	0.0	0		137.0	70.0	0.510949	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	C	1.691	-0.503992	0.04261	0.0	1.16E-4	ENSG00000164961	ENST00000523273	.	.	.	5.28	-0.0402	0.13872	.	.	.	.	.	T	0.52451	0.1735	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44375	-0.9332	4	.	.	.	-2.3241	7.0005	0.24807	0.486:0.2384:0.0:0.2756	.	.	.	.	H	560	.	.	R	-	2	0	KIAA0196	126125270	0.951000	0.32395	0.914000	0.36105	0.259000	0.26198	0.151000	0.16283	0.347000	0.23924	-1.268000	0.01426	CGT	.	.	weak		0.303	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3391458	3391458	+	Missense_Mutation	SNP	G	G	A	rs200941005	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:3391458G>A	ENST00000324266.5	+	2	259	c.64G>A	c.(64-66)Gcg>Acg	p.A22T	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.A22T	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	22					vesicle-mediated transport (GO:0016192)												CCCTCAGCTCGCGCCTCCGGA	0.652													G|||	7	0.00139776	0.0008	0.0	5008	,	,		8905	0.0		0.004	False		,,,				2504	0.002				p.A22T		Atlas-SNP	.											.	.	.	.	0			c.G64A						PASS	.	G	THR/ALA	2,4368		0,2,2183	16.0	16.0	16.0		64	2.5	0.0	2		16	25,8533		0,25,4254	yes	missense	TTC15	NM_016030.5	58	0,27,6437	AA,AG,GG		0.2921,0.0458,0.2088	benign	22/736	3391458	27,12901	2185	4279	6464	SO:0001583	missense	51112	exon2			CAGCTCGCGCCTC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.64G>A	2.37:g.3391458G>A	ENSP00000324318:p.Ala22Thr	43.0	0.0	0		46.0	34.0	0.73913	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	8.692	0.907612	0.17833	4.58E-4	0.002921	ENSG00000171853	ENST00000382110;ENST00000324266	T;T	0.68025	-0.3;-0.3	4.34	2.46	0.29980	.	1.827870	0.02663	N	0.107730	T	0.41627	0.1167	L	0.29908	0.895	0.09310	N	1	B;P	0.42692	0.429;0.787	B;B	0.34418	0.019;0.182	T	0.38693	-0.9649	10	0.14656	T	0.56	.	5.7337	0.18055	0.1029:0.0:0.7068:0.1903	.	22;22	Q8WVT3;Q53S18	TPC12_HUMAN;.	T	22	ENSP00000371544:A22T;ENSP00000324318:A22T	ENSP00000324318:A22T	A	+	1	0	TTC15	3370465	0.027000	0.19231	0.000000	0.03702	0.001000	0.01503	1.104000	0.31074	0.524000	0.28502	0.563000	0.77884	GCG	G|0.998;A|0.002	0.002	strong		0.652	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
GALNT14	79623	hgsc.bcm.edu	37	2	31348076	31348076	+	Intron	SNP	G	G	A	rs41280621	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:31348076G>A	ENST00000349752.5	-	1	769				GALNT14_ENST00000324589.5_Missense_Mutation_p.A58V|GALNT14_ENST00000406653.1_5'UTR|GALNT14_ENST00000420311.2_Intron|GALNT14_ENST00000356174.3_Intron	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					CACCTGAGGCGCCCAAGGGCT	0.512													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		20381	0.0		0.004	False		,,,				2504	0.0051				p.A58V		Atlas-SNP	.											.	GALNT14	103	.	0			c.C173T						PASS	.																																			SO:0001627	intron_variant	79623	exon2			TGAGGCGCCCAAG	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.129+12747C>T	2.37:g.31348076G>A		37.0	0.0	0		36.0	15.0	0.416667	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	8.995	0.978610	0.18812	.	.	ENSG00000158089	ENST00000324589	T	0.58060	0.36	3.94	-7.88	0.01178	.	16.563700	0.00166	N	0.000002	T	0.23289	0.0563	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.30078	T	0.28	.	3.8926	0.09125	0.3307:0.1169:0.4366:0.1157	rs41280621	58	Q96FL9-3	.	V	58	ENSP00000314500:A58V	ENSP00000314500:A58V	A	-	2	0	GALNT14	31201580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.055000	0.01397	-1.937000	0.01047	-4.460000	0.00005	GCG	G|0.994;A|0.006	0.006	strong		0.512	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
MAMDC2	256691	hgsc.bcm.edu	37	9	72723204	72723204	+	Missense_Mutation	SNP	G	G	A	rs139498917	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:72723204G>A	ENST00000377182.4	+	3	843	c.226G>A	c.(226-228)Gag>Aag	p.E76K	MAMDC2-AS1_ENST00000591368.1_RNA|MAMDC2-AS1_ENST00000414515.3_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	76	MAM 1. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						CTTACAGGCTGAGGAATGGAG	0.488													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		17888	0.0		0.003	False		,,,				2504	0.0				p.E76K		Atlas-SNP	.											.	MAMDC2	55	.	0			c.G226A						PASS	.	G	LYS/GLU	4,4402	8.1+/-20.4	0,4,2199	116.0	108.0	111.0		226	5.9	1.0	9	dbSNP_134	111	26,8574	19.2+/-60.6	0,26,4274	yes	missense	MAMDC2	NM_153267.4	56	0,30,6473	AA,AG,GG		0.3023,0.0908,0.2307	possibly-damaging	76/687	72723204	30,12976	2203	4300	6503	SO:0001583	missense	256691	exon3			CAGGCTGAGGAAT	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.226G>A	9.37:g.72723204G>A	ENSP00000366387:p.Glu76Lys	149.0	0.0	0		125.0	63.0	0.504	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	37	CCDS6631.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.73	2.323034	0.41096	9.08E-4	0.003023	ENSG00000165072	ENST00000377182	T	0.01981	4.52	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.391658	0.29916	N	0.010874	T	0.04588	0.0125	L	0.59436	1.845	0.39469	D	0.967694	P	0.41345	0.746	B	0.41988	0.372	T	0.52866	-0.8518	10	0.07813	T	0.8	-29.7414	20.3324	0.98724	0.0:0.0:1.0:0.0	.	76	Q7Z304	MAMC2_HUMAN	K	76	ENSP00000366387:E76K	ENSP00000366387:E76K	E	+	1	0	MAMDC2	71913024	1.000000	0.71417	0.999000	0.59377	0.757000	0.42996	4.560000	0.60802	2.799000	0.96334	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	strong		0.488	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
UBR4	23352	hgsc.bcm.edu	37	1	19500088	19500088	+	Silent	SNP	A	A	G	rs41273197	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19500088A>G	ENST00000375254.3	-	23	3037	c.3010T>C	c.(3010-3012)Ttg>Ctg	p.L1004L	UBR4_ENST00000375217.2_Silent_p.L1004L|UBR4_ENST00000375267.2_Silent_p.L1004L|UBR4_ENST00000375226.2_Silent_p.L1004L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1004					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CACAGTATCAAGAAGTAATAT	0.448													A|||	9	0.00179712	0.0	0.0043	5008	,	,		19762	0.0		0.003	False		,,,				2504	0.0031				p.L1004L		Atlas-SNP	.											.	UBR4	415	.	0			c.T3010C						PASS	.	A		12,4394	17.9+/-39.9	0,12,2191	83.0	78.0	80.0		3010	-0.9	1.0	1	dbSNP_127	80	76,8524	43.6+/-101.6	2,72,4226	no	coding-synonymous	UBR4	NM_020765.2		2,84,6417	GG,GA,AA		0.8837,0.2724,0.6766		1004/5184	19500088	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon23			GTATCAAGAAGTA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3010T>C	1.37:g.19500088A>G		78.0	0.0	0		112.0	59.0	0.526786	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			A|0.995;G|0.005	0.005	strong		0.448	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
CWF19L2	143884	hgsc.bcm.edu	37	11	107309826	107309826	+	Silent	SNP	C	C	T	rs201136952		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:107309826C>T	ENST00000282251.5	-	6	681	c.654G>A	c.(652-654)tcG>tcA	p.S218S	CWF19L2_ENST00000433523.1_Silent_p.S218S	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	218							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CTTTAGTAATCGATGACACAC	0.388													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13512	0.0		0.0	False		,,,				2504	0.0				p.S218S		Atlas-SNP	.											CWF19L2_ENST00000282251,NS,carcinoma,0,2	CWF19L2	135	2	0			c.G654A						PASS	.						78.0	67.0	71.0					11																	107309826		2201	4298	6499	SO:0001819	synonymous_variant	143884	exon6			AGTAATCGATGAC	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.654G>A	11.37:g.107309826C>T		44.0	0.0	0		32.0	8.0	0.25	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	37	CCDS8336.2																																																																																			C|1.000;T|0.000	0.000	strong		0.388	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34789443	34789443	+	Missense_Mutation	SNP	C	C	G	rs369670668		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34789443C>G	ENST00000192788.5	+	2	229	c.58C>G	c.(58-60)Ctt>Gtt	p.L20V	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.L20V|Y_RNA_ENST00000383990.1_RNA	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	20							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CACTAAGAATCTTTCCCCAGA	0.438																																					p.L20V		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C58G						PASS	.	C	VAL/LEU	0,3714		0,0,1857	42.0	42.0	42.0		58	3.9	1.0	6		42	1,8213		0,1,4106	no	missense	UHRF1BP1	NM_017754.3	32	0,1,5963	GG,GC,CC		0.0122,0.0,0.0084	probably-damaging	20/1441	34789443	1,11927	1857	4107	5964	SO:0001583	missense	54887	exon2			AAGAATCTTTCCC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.58C>G	6.37:g.34789443C>G	ENSP00000192788:p.Leu20Val	115.0	0.0	0		114.0	14.0	0.122807	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184160	0.78677	0.0	1.22E-4	ENSG00000065060	ENST00000192788;ENST00000452449	D;D	0.85171	-1.95;-1.95	5.79	3.93	0.45458	.	0.000000	0.64402	D	0.000001	D	0.89015	0.6595	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88591	0.3143	10	0.59425	D	0.04	-15.3813	11.3038	0.49323	0.0:0.8033:0.1278:0.0689	.	20	Q6BDS2	URFB1_HUMAN	V	20	ENSP00000192788:L20V;ENSP00000400628:L20V	ENSP00000192788:L20V	L	+	1	0	UHRF1BP1	34897421	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.312000	0.51927	2.732000	0.93576	0.557000	0.71058	CTT	.	.	weak		0.438	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
PVRL1	5818	hgsc.bcm.edu	37	11	119549473	119549473	+	Missense_Mutation	SNP	C	C	T	rs200377205		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119549473C>T	ENST00000264025.3	-	2	612	c.82G>A	c.(82-84)Gtc>Atc	p.V28I	PVRL1_ENST00000340882.2_Missense_Mutation_p.V28I|PVRL1_ENST00000341398.2_Missense_Mutation_p.V28I|PVRL1_ENST00000524510.1_5'UTR	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	28					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		TGGGAGTGGACGCCTGGCCAG	0.587																																					p.V28I		Atlas-SNP	.											.	PVRL1	133	.	0			c.G82A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	0,4398		0,0,2199	52.0	36.0	42.0		82,82,82	-2.6	0.0	11		42	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,missense	PVRL1	NM_203286.1,NM_203285.1,NM_002855.4	29,29,29	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	28/353,28/459,28/518	119549473	1,12987	2199	4295	6494	SO:0001583	missense	5818	exon2			AGTGGACGCCTGG	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.82G>A	11.37:g.119549473C>T	ENSP00000264025:p.Val28Ile	34.0	0.0	0		40.0	9.0	0.225	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853973	0.32791	0.0	1.16E-4	ENSG00000110400	ENST00000341398;ENST00000264025;ENST00000340882	T;T;T	0.75154	-0.84;-0.91;-0.83	5.45	-2.56	0.06268	Immunoglobulin-like (1);	0.453783	0.23048	N	0.052524	T	0.50171	0.1600	N	0.19112	0.55	0.09310	N	1	B;B;B	0.22604	0.023;0.029;0.072	B;B;B	0.11329	0.004;0.001;0.006	T	0.32375	-0.9909	9	.	.	.	.	7.776	0.29037	0.0:0.3707:0.151:0.4783	.	28;28;28	Q15223-3;Q15223;Q15223-2	.;PVRL1_HUMAN;.	I	28	ENSP00000344974:V28I;ENSP00000264025:V28I;ENSP00000345289:V28I	.	V	-	1	0	PVRL1	119054683	0.001000	0.12720	0.013000	0.15412	0.047000	0.14425	0.252000	0.18278	-0.358000	0.08162	-0.373000	0.07131	GTC	C|0.996;T|0.005	0.005	weak		0.587	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
EP400	57634	hgsc.bcm.edu	37	12	132504639	132504639	+	Silent	SNP	C	C	T	rs147615479	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132504639C>T	ENST00000333577.4	+	23	4540	c.4431C>T	c.(4429-4431)acC>acT	p.T1477T	EP400_ENST00000389561.2_Silent_p.T1441T|EP400_ENST00000330386.6_Silent_p.T1441T|EP400_ENST00000332482.4_Silent_p.T1404T|EP400_ENST00000389562.2_Silent_p.T1440T			Q96L91	EP400_HUMAN	E1A binding protein p400	1477					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AGGGTCGCACCGTGGCTTTCC	0.647													C|||	12	0.00239617	0.0	0.0058	5008	,	,		14876	0.0		0.007	False		,,,				2504	0.001				p.T1441T		Atlas-SNP	.											.	EP400	370	.	0			c.C4323T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	66.0	63.0	64.0		4323	-11.1	0.4	12	dbSNP_134	64	96,8504	54.0+/-114.7	0,96,4204	no	coding-synonymous	EP400	NM_015409.4		0,105,6398	TT,TC,CC		1.1163,0.2043,0.8073		1441/3124	132504639	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon22			TCGCACCGTGGCT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.4431C>T	12.37:g.132504639C>T		57.0	0.0	0		48.0	30.0	0.625	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.994;T|0.006	0.006	strong		0.647	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
STPG2	285555	hgsc.bcm.edu	37	4	98902403	98902403	+	Missense_Mutation	SNP	T	T	C	rs76740552	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:98902403T>C	ENST00000295268.3	-	6	768	c.679A>G	c.(679-681)Aag>Gag	p.K227E		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	227																	TTCAAAGACTTGAGAGCAGTT	0.403													T|||	34	0.00678914	0.025	0.0014	5008	,	,		16243	0.0		0.0	False		,,,				2504	0.0				p.K227E		Atlas-SNP	.											.	.	.	.	0			c.A679G						PASS	.	T	GLU/LYS	70,4336	63.5+/-100.7	0,70,2133	152.0	149.0	150.0		679	1.6	0.0	4	dbSNP_131	150	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C4orf37	NM_174952.2	56	0,72,6431	CC,CT,TT		0.0233,1.5887,0.5536	benign	227/460	98902403	72,12934	2203	4300	6503	SO:0001583	missense	285555	exon6			AAGACTTGAGAGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.679A>G	4.37:g.98902403T>C	ENSP00000295268:p.Lys227Glu	134.0	0.0	0		92.0	56.0	0.608696	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	0.042	-1.280208	0.01398	0.015887	2.33E-4	ENSG00000163116	ENST00000295268	T	0.11169	2.8	5.41	1.6	0.23607	.	0.284305	0.30401	N	0.009707	T	0.00906	0.0030	N	0.03154	-0.405	0.19575	N	0.999964	B	0.11235	0.004	B	0.16289	0.015	T	0.41592	-0.9500	10	0.02654	T	1	-29.499	2.4269	0.04461	0.2322:0.378:0.0:0.3898	.	227	Q8N412	CD037_HUMAN	E	227	ENSP00000295268:K227E	ENSP00000295268:K227E	K	-	1	0	C4orf37	99121426	0.446000	0.25665	0.001000	0.08648	0.381000	0.30169	0.483000	0.22292	0.332000	0.23536	0.460000	0.39030	AAG	T|0.994;C|0.006	0.006	strong		0.403	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
GRHL2	79977	hgsc.bcm.edu	37	8	102570830	102570830	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:102570830G>A	ENST00000251808.3	+	4	806	c.468G>A	c.(466-468)acG>acA	p.T156T	GRHL2_ENST00000395927.1_Silent_p.T140T	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	156					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			CGGGAATCACGGTGGTGAAAG	0.522																																					p.T156T		Atlas-SNP	.											GRHL2,right_lower_lobe,carcinoma,0,1	GRHL2	68	1	0			c.G468A						PASS	.						107.0	100.0	103.0					8																	102570830		2203	4300	6503	SO:0001819	synonymous_variant	79977	exon4			AATCACGGTGGTG	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.468G>A	8.37:g.102570830G>A		101.0	0.0	0		119.0	33.0	0.277311	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																			.	.	none		0.522	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
TIAM2	26230	hgsc.bcm.edu	37	6	155458562	155458562	+	Silent	SNP	C	C	T	rs374521659		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155458562C>T	ENST00000461783.3	+	7	2719	c.1446C>T	c.(1444-1446)acC>acT	p.T482T	TIAM2_ENST00000360366.4_Silent_p.T482T|TIAM2_ENST00000318981.5_Silent_p.T482T|TIAM2_ENST00000529824.2_Silent_p.T482T|TIAM2_ENST00000456144.1_Silent_p.T482T|TIAM2_ENST00000367174.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	482					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CTACAGAAACCGCCGAGTCCA	0.527																																					p.T482T		Atlas-SNP	.											.	TIAM2	161	.	0			c.C1446T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	89.0	97.0	94.0		1446	-12.2	0.0	6		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TIAM2	NM_012454.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		482/1702	155458562	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon4			AGAAACCGCCGAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.1446C>T	6.37:g.155458562C>T		89.0	0.0	0		86.0	33.0	0.383721	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			.	.	weak		0.527	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
FCRL3	115352	hgsc.bcm.edu	37	1	157670258	157670258	+	Missense_Mutation	SNP	G	G	C	rs201961888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:157670258G>C	ENST00000368184.3	-	2	313	c.22C>G	c.(22-24)Ctg>Gtg	p.L8V	FCRL3_ENST00000473231.1_5'Flank|FCRL3_ENST00000368186.5_Missense_Mutation_p.L8V	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					CTCAGGATCAGCAGCAGCAGC	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		16345	0.0		0.001	False		,,,				2504	0.0				p.L8V		Atlas-SNP	.											.	FCRL3	163	.	0			c.C22G						PASS	.						46.0	49.0	48.0					1																	157670258		2203	4300	6503	SO:0001583	missense	115352	exon2			GGATCAGCAGCAG	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.22C>G	1.37:g.157670258G>C	ENSP00000357167:p.Leu8Val	163.0	0.0	0		132.0	43.0	0.325758	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.556	0.470796	0.12461	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.66638	-0.22;-0.22	3.6	2.69	0.31865	.	0.702293	0.10648	U	0.650160	T	0.69913	0.3164	M	0.70842	2.15	0.40781	D	0.98317	D;D	0.76494	0.999;0.999	D;D	0.80764	0.986;0.994	T	0.67503	-0.5654	10	0.45353	T	0.12	.	6.8585	0.24054	0.1278:0.0:0.8722:0.0	.	8;8	Q96P31;Q96P31-6	FCRL3_HUMAN;.	V	8	ENSP00000357169:L8V;ENSP00000357167:L8V	ENSP00000292392:L8V	L	-	1	2	FCRL3	155936882	0.995000	0.38212	0.996000	0.52242	0.930000	0.56654	1.824000	0.39072	1.095000	0.41419	0.467000	0.42956	CTG	G|1.000;C|0.000	0.000	strong		0.547	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939	
SLC16A11	162515	hgsc.bcm.edu	37	17	6946357	6946357	+	Missense_Mutation	SNP	C	C	A	rs75636181	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6946357C>A	ENST00000308009.1	-	2	647	c.310G>T	c.(310-312)Gcc>Tcc	p.A104S	SLC16A11_ENST00000447225.1_Missense_Mutation_p.A80S	NM_153357.1	NP_699188.1	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11	104					lipid metabolic process (GO:0006629)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(2)|ovary(1)|skin(2)	9						ACGGGGCGGGCCCCCCAGCGC	0.692													.|||	101	0.0201677	0.0023	0.0303	5008	,	,		13501	0.0		0.0676	False		,,,				2504	0.0092				p.A104S		Atlas-SNP	.											SLC16A11,NS,carcinoma,0,1	SLC16A11	25	1	0			c.G310T						PASS	.	C	SER/ALA	70,4266		0,70,2098	10.0	14.0	13.0		310	3.1	1.0	17	dbSNP_131	13	545,7977		24,497,3740	no	missense	SLC16A11	NM_153357.1	99	24,567,5838	AA,AC,CC		6.3952,1.6144,4.783	benign	104/472	6946357	615,12243	2168	4261	6429	SO:0001583	missense	162515	exon2			GGCGGGCCCCCCA	AK074674	CCDS11086.1	17p13.2	2013-07-18	2013-07-18		ENSG00000174326	ENSG00000174326		"""Solute carriers"""	23093	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 11"""	615765	"""solute carrier family 16 (monocarboxylic acid transporters), member 11"""				Standard	NM_153357		Approved	FLJ90193, MCT11	uc002gei.1	Q8NCK7	OTTHUMG00000102087	ENST00000308009.1:c.310G>T	17.37:g.6946357C>A	ENSP00000310490:p.Ala104Ser	68.0	0.0	0		28.0	17.0	0.607143	NM_153357		Missense_Mutation	SNP	ENST00000308009.1	37	CCDS11086.1	71	0.03250915750915751	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	53	0.06992084432717678	C	10.57	1.386498	0.25031	0.016144	0.063952	ENSG00000174326	ENST00000308009;ENST00000447225	T;T	0.37411	1.2;1.2	5.18	3.09	0.35607	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.319287	0.34046	N	0.004302	T	0.01156	0.0038	N	0.03238	-0.38	0.38818	P	0.04442900000000005	B	0.15719	0.014	B	0.20955	0.032	T	0.08743	-1.0707	9	0.27785	T	0.31	.	11.0985	0.48160	0.5302:0.4698:0.0:0.0	.	104	Q8NCK7	MOT11_HUMAN	S	104;80	ENSP00000310490:A104S;ENSP00000394449:A80S	ENSP00000310490:A104S	A	-	1	0	SLC16A11	6887081	0.001000	0.12720	1.000000	0.80357	0.945000	0.59286	-0.023000	0.12456	0.676000	0.31285	0.555000	0.69702	GCC	C|0.967;A|0.033	0.033	strong		0.692	SLC16A11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219921.1	NM_153357	
EPPK1	83481	hgsc.bcm.edu	37	8	144943384	144943384	+	Silent	SNP	G	G	A	rs189024404	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144943384G>A	ENST00000525985.1	-	2	4109	c.4038C>T	c.(4036-4038)ctC>ctT	p.L1346L				P58107	EPIPL_HUMAN	epiplakin 1	1346						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCTGTGGCACGAGCCCCTTCT	0.697													G|||	99	0.0197684	0.0681	0.0101	5008	,	,		16771	0.0		0.002	False		,,,				2504	0.0				p.L1346L		Atlas-SNP	.											.	EPPK1	199	.	0			c.C4038T						PASS	.	G		125,3773		1,123,1825	18.0	22.0	21.0		4038	-8.7	0.0	8		21	7,8235		0,7,4114	no	coding-synonymous	EPPK1	NM_031308.1		1,130,5939	AA,AG,GG		0.0849,3.2068,1.0873		1346/2420	144943384	132,12008	1949	4121	6070	SO:0001819	synonymous_variant	83481	exon1			TGGCACGAGCCCC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4038C>T	8.37:g.144943384G>A		37.0	0.0	0		48.0	30.0	0.625	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.988;A|0.012	0.012	strong		0.697	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ZBTB20	26137	hgsc.bcm.edu	37	3	114058008	114058008	+	Silent	SNP	G	G	T	rs139619357	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:114058008G>T	ENST00000474710.1	-	5	2248	c.2070C>A	c.(2068-2070)acC>acA	p.T690T	ZBTB20_ENST00000464560.1_Silent_p.T617T|ZBTB20_ENST00000462705.1_Silent_p.T617T|ZBTB20_ENST00000481632.1_Silent_p.T617T|ZBTB20_ENST00000393785.2_Silent_p.T617T|ZBTB20_ENST00000357258.3_Silent_p.T617T|ZBTB20_ENST00000471418.1_Silent_p.T617T	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	690						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		CTGCAGGGGGGGTCCCATTGC	0.642													G|||	2	0.000399361	0.0	0.0	5008	,	,		15690	0.0		0.0	False		,,,				2504	0.002				p.T690T	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											.	ZBTB20	157	.	0			c.C2070A						PASS	.	G	,,,,,,	3,4403	6.2+/-15.9	0,3,2200	64.0	62.0	63.0		2070,1851,1851,1851,1851,1851,1851	5.3	1.0	3	dbSNP_134	63	15,8585	11.9+/-42.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZBTB20	NM_001164342.1,NM_001164343.1,NM_001164344.1,NM_001164345.1,NM_001164346.1,NM_001164347.1,NM_015642.4	,,,,,,	0,18,6485	TT,TG,GG		0.1744,0.0681,0.1384	,,,,,,	690/742,617/669,617/669,617/669,617/669,617/669,617/669	114058008	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	26137	exon5			AGGGGGGGTCCCA	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13503	protein-coding gene	gene with protein product		606025	"""zinc finger protein 288"""	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.2070C>A	3.37:g.114058008G>T		126.0	0.0	0		104.0	45.0	0.432692	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	37	CCDS54626.1																																																																																			G|0.999;T|0.001	0.001	strong		0.642	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642	
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17367354G>A	ENST00000252597.3	-	9	1569	c.1396C>T	c.(1396-1398)Ctg>Ttg	p.L466L	USHBP1_ENST00000431146.2_Silent_p.L402L|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TGGGTCCCCAGAATGGCCTGC	0.612													G|||	21	0.00419329	0.0	0.013	5008	,	,		18612	0.0		0.007	False		,,,				2504	0.0051				p.L466L		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1396T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	74.0	77.0	76.0		1396	3.8	1.0	19	dbSNP_134	76	96,8504	51.9+/-112.3	0,96,4204	no	coding-synonymous	USHBP1	NM_031941.3		0,107,6396	AA,AG,GG		1.1163,0.2497,0.8227		466/704	17367354	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon9			TCCCCAGAATGGC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1396C>T	19.37:g.17367354G>A		60.0	0.0	0		54.0	31.0	0.574074	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
TSHZ3	57616	hgsc.bcm.edu	37	19	31770506	31770506	+	Missense_Mutation	SNP	C	C	T	rs111618794	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:31770506C>T	ENST00000240587.4	-	2	520	c.193G>A	c.(193-195)Gcc>Acc	p.A65T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	65					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GAAAACTCGGCGGCCGGGGAG	0.592													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15202	0.0		0.003	False		,,,				2504	0.0				p.A65T		Atlas-SNP	.											TSHZ3_ENST00000240587,NS,carcinoma,+2,1	TSHZ3	549	1	0			c.G193A						PASS	.	C	THR/ALA	0,3914		0,0,1957	32.0	34.0	34.0		193	5.9	0.2	19	dbSNP_132	34	14,8248		0,14,4117	yes	missense	TSHZ3	NM_020856.2	58	0,14,6074	TT,TC,CC		0.1695,0.0,0.115	possibly-damaging	65/1082	31770506	14,12162	1957	4131	6088	SO:0001583	missense	57616	exon2			ACTCGGCGGCCGG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.193G>A	19.37:g.31770506C>T	ENSP00000240587:p.Ala65Thr	71.0	0.0	0		41.0	19.0	0.463415	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	16.97	3.269545	0.59540	0.0	0.001695	ENSG00000121297	ENST00000240587	T	0.12984	2.63	5.92	5.92	0.95590	.	0.000000	0.64402	U	0.000001	T	0.24736	0.0600	L	0.40543	1.245	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.00394	-1.1767	10	0.87932	D	0	-15.0968	20.3116	0.98642	0.0:1.0:0.0:0.0	.	65	Q63HK5	TSH3_HUMAN	T	65	ENSP00000240587:A65T	ENSP00000240587:A65T	A	-	1	0	TSHZ3	36462346	1.000000	0.71417	0.217000	0.23759	0.270000	0.26580	5.737000	0.68606	2.793000	0.96121	0.650000	0.86243	GCC	C|0.998;T|0.002	0.002	strong		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:136834138T>C	ENST00000394945.1	-	2	279	c.110A>G	c.(109-111)aAt>aGt	p.N37S	SPOCK1_ENST00000282223.7_Missense_Mutation_p.N37S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	37					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTCTAGGAAATTGCCGTGGTT	0.682													T|||	19	0.00379393	0.0	0.0058	5008	,	,		9286	0.0		0.0129	False		,,,				2504	0.002				p.N37S		Atlas-SNP	.											.	SPOCK1	58	.	0			c.A110G						PASS	.	T	SER/ASN	9,4397		0,9,2194	22.0	21.0	22.0		110	3.7	1.0	5	dbSNP_132	22	106,8492		3,100,4196	yes	missense	SPOCK1	NM_004598.3	46	3,109,6390	CC,CT,TT		1.2328,0.2043,0.8843	benign	37/440	136834138	115,12889	2203	4299	6502	SO:0001583	missense	6695	exon2			AGGAAATTGCCGT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.110A>G	5.37:g.136834138T>C	ENSP00000378401:p.Asn37Ser	44.0	0.0	0		41.0	20.0	0.487805	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	24.2	4.510460	0.85389	0.002043	0.012328	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.58940	0.3;0.3;0.34	3.66	3.66	0.41972	.	0.344437	0.23803	N	0.044419	T	0.33498	0.0865	L	0.51914	1.62	0.27215	N	0.959807	B	0.15930	0.015	B	0.14578	0.011	T	0.44112	-0.9349	10	0.56958	D	0.05	.	10.3639	0.44012	0.0:0.0:0.0:1.0	.	37	Q08629	TICN1_HUMAN	S	37	ENSP00000378401:N37S;ENSP00000282223:N37S;ENSP00000424517:N37S	ENSP00000282223:N37S	N	-	2	0	SPOCK1	136862037	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.481000	0.53179	1.439000	0.47511	0.379000	0.24179	AAT	T|0.991;C|0.009	0.009	strong		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
USP7	7874	hgsc.bcm.edu	37	16	8989511	8989511	+	Silent	SNP	C	C	T	rs61731196	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:8989511C>T	ENST00000344836.4	-	27	3105	c.2907G>A	c.(2905-2907)acG>acA	p.T969T	USP7_ENST00000535863.1_Silent_p.T870T|USP7_ENST00000381886.4_Silent_p.T953T	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	969					maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CTATTCGAAACGTCCGGCTCG	0.418													C|||	11	0.00219649	0.0	0.0014	5008	,	,		17036	0.0		0.0099	False		,,,				2504	0.0				p.T969T		Atlas-SNP	.											.	USP7	116	.	0			c.G2907A						PASS	.	C		7,4387	12.9+/-30.5	0,7,2190	79.0	77.0	77.0		2907	2.4	1.0	16	dbSNP_129	77	91,8509	51.1+/-111.2	0,91,4209	no	coding-synonymous	USP7	NM_003470.2		0,98,6399	TT,TC,CC		1.0581,0.1593,0.7542		969/1103	8989511	98,12896	2197	4300	6497	SO:0001819	synonymous_variant	7874	exon27			TCGAAACGTCCGG	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.2907G>A	16.37:g.8989511C>T		94.0	0.0	0		84.0	38.0	0.452381	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																			C|0.994;T|0.006	0.006	strong		0.418	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		
MTERF4	130916	hgsc.bcm.edu	37	2	242039210	242039210	+	Missense_Mutation	SNP	G	G	A	rs143756138	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242039210G>A	ENST00000391980.2	-	2	179	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	MTERFD2_ENST00000495694.1_Missense_Mutation_p.R41C|MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000407095.3_Missense_Mutation_p.R41C	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		41					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		GTCAGTTTGCGCAACAAAGAA	0.512													G|||	2	0.000399361	0.0	0.0014	5008	,	,		19876	0.0		0.001	False		,,,				2504	0.0				p.R41C		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C121T						PASS	.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	63.0	62.0	62.0		121	1.7	0.0	2	dbSNP_134	62	4,8596	3.7+/-12.6	0,4,4296	yes	missense	MTERFD2	NM_182501.3	180	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	probably-damaging	41/382	242039210	5,13001	2203	4300	6503	SO:0001583	missense	130916	exon2			GTTTGCGCAACAA																												ENST00000391980.2:c.121C>T	2.37:g.242039210G>A	ENSP00000375840:p.Arg41Cys	79.0	0.0	0		93.0	42.0	0.451613	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.21	1.570481	0.28003	2.27E-4	4.65E-4	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.54479	0.57;0.66;2.42;1.26;1.28;0.72	4.57	1.73	0.24493	.	0.943497	0.08723	N	0.903139	T	0.28896	0.0717	N	0.08118	0	0.09310	N	1	B;B	0.26577	0.029;0.153	B;B	0.15052	0.005;0.012	T	0.16394	-1.0404	10	0.37606	T	0.19	-22.0841	6.2517	0.20850	0.337:0.0:0.663:0.0	.	41;41	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	C	41;41;41;34;41;20	ENSP00000419315:R41C;ENSP00000385183:R41C;ENSP00000375840:R41C;ENSP00000409023:R34C;ENSP00000385630:R41C;ENSP00000393063:R20C	ENSP00000241527:R41C	R	-	1	0	MTERFD2	241687883	0.001000	0.12720	0.001000	0.08648	0.429000	0.31625	0.448000	0.21726	0.047000	0.15862	0.591000	0.81541	CGC	G|0.999;A|0.001	0.001	strong		0.512	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
DNAH10	196385	hgsc.bcm.edu	37	12	124417973	124417973	+	Silent	SNP	C	C	T	rs56219209	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124417973C>T	ENST00000409039.3	+	76	13063	c.13038C>T	c.(13036-13038)aaC>aaT	p.N4346N	CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_Intron|DNAH10_ENST00000538983.1_3'UTR|RP11-380L11.3_ENST00000602292.1_RNA	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4346					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCGGAAGAACGGCTGGCCAC	0.622													C|||	40	0.00798722	0.0008	0.0072	5008	,	,		19026	0.005		0.0189	False		,,,				2504	0.0102				p.N4346N		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13038T						PASS	.	C		14,3946		0,14,1966	35.0	38.0	37.0		13038	-2.1	1.0	12	dbSNP_129	37	168,8134		1,166,3984	no	coding-synonymous	DNAH10	NM_207437.3		1,180,5950	TT,TC,CC		2.0236,0.3535,1.4843		4346/4472	124417973	182,12080	1980	4151	6131	SO:0001819	synonymous_variant	196385	exon76			GAAGAACGGCTGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.13038C>T	12.37:g.124417973C>T		43.0	0.0	0		57.0	27.0	0.473684	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.985;T|0.015	0.015	strong		0.622	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
VPS9D1	9605	hgsc.bcm.edu	37	16	89783205	89783205	+	Silent	SNP	G	G	A	rs118114589	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89783205G>A	ENST00000389386.3	-	3	325	c.201C>T	c.(199-201)gaC>gaT	p.D67D	VPS9D1-AS1_ENST00000562298.1_RNA|VPS9D1_ENST00000561976.1_5'UTR|VPS9D1-AS1_ENST00000562866.1_RNA	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	67					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										TCTTGGAGGTGTCGGGGGGCA	0.597													g|||	127	0.0253594	0.0015	0.0173	5008	,	,		12625	0.001		0.0249	False		,,,				2504	0.089				p.D67D		Atlas-SNP	.											.	.	.	.	0			c.C201T						PASS	.			16,3858		0,16,1921	17.0	20.0	19.0		201	-1.8	0.1	16	dbSNP_132	19	197,8037		1,195,3921	no	coding-synonymous	C16orf7	NM_004913.2		1,211,5842	AA,AG,GG		2.3925,0.413,1.7592		67/632	89783205	213,11895	1937	4117	6054	SO:0001819	synonymous_variant	9605	exon3			GGAGGTGTCGGGG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.201C>T	16.37:g.89783205G>A		60.0	0.0	0		52.0	29.0	0.557692	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
OR51E1	143503	hgsc.bcm.edu	37	11	4674343	4674343	+	Missense_Mutation	SNP	G	G	A	rs139501861	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4674343G>A	ENST00000396952.5	+	2	1237	c.587G>A	c.(586-588)cGg>cAg	p.R196Q	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGATATCCGGGTCAATGTC	0.488													G|||	9	0.00179712	0.0	0.0043	5008	,	,		24525	0.0		0.005	False		,,,				2504	0.001				p.R196Q		Atlas-SNP	.											OR51E1,caecum,carcinoma,-1,1	OR51E1	67	1	0			c.G587A						scavenged	.	G	GLN/ARG	11,4391	17.9+/-39.9	0,11,2190	237.0	206.0	216.0		587	-2.6	0.3	11	dbSNP_134	216	62,8534	38.8+/-94.9	0,62,4236	yes	missense	OR51E1	NM_152430.3	43	0,73,6426	AA,AG,GG		0.7213,0.2499,0.5616	possibly-damaging	196/319	4674343	73,12925	2201	4298	6499	SO:0001583	missense	143503	exon2			ATATCCGGGTCAA	AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"""GPCR / Class A : Olfactory receptors"""	15194	protein-coding gene	gene with protein product		611267	"""olfactory receptor, family 51, subfamily E, member 1 pseudogene"""	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.587G>A	11.37:g.4674343G>A	ENSP00000380155:p.Arg196Gln	143.0	1.0	0.00699301		138.0	74.0	0.536232	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	9.562	1.118610	0.20877	0.002499	0.007213	ENSG00000180785	ENST00000396952	T	0.37752	1.18	4.98	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	1.290730	0.05102	N	0.487404	T	0.33644	0.0870	L	0.50919	1.6	0.09310	N	1	P	0.43431	0.807	P	0.48270	0.572	T	0.50972	-0.8764	10	0.54805	T	0.06	.	11.1371	0.48381	0.5891:0.0:0.4109:0.0	.	195	Q8TCB6	O51E1_HUMAN	Q	196	ENSP00000380155:R196Q	ENSP00000380155:R196Q	R	+	2	0	OR51E1	4630919	0.000000	0.05858	0.286000	0.24833	0.395000	0.30598	-2.797000	0.00763	-0.557000	0.06126	-0.736000	0.03550	CGG	G|0.996;A|0.004	0.004	strong		0.488	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430	
NPC2	10577	hgsc.bcm.edu	37	14	74951269	74951269	+	Missense_Mutation	SNP	T	T	C	rs142075589		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74951269T>C	ENST00000555619.1	-	3	449	c.212A>G	c.(211-213)aAg>aGg	p.K71R	NPC2_ENST00000434013.2_Missense_Mutation_p.K71R|NPC2_ENST00000541064.1_Missense_Mutation_p.K71R|NPC2_ENST00000557510.1_Missense_Mutation_p.K71R|NPC2_ENST00000238633.2_Missense_Mutation_p.K71R	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	71					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|glycolipid transport (GO:0046836)|intracellular cholesterol transport (GO:0032367)|intracellular sterol transport (GO:0032366)|phospholipid transport (GO:0015914)|regulation of isoprenoid metabolic process (GO:0019747)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.00149)		CACCACGGCCTTGCTGCTTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		18393	0.0		0.001	False		,,,				2504	0.0				p.K71R	Pancreas(93;260 1497 8575 30964 48133)	Atlas-SNP	.											.	NPC2	9	.	0			c.A212G						PASS	.	T	ARG/LYS	0,4406		0,0,2203	105.0	101.0	102.0		212	4.2	0.9	14	dbSNP_134	102	2,8598		0,2,4298	yes	missense	NPC2	NM_006432.3	26	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	possibly-damaging	71/152	74951269	2,13004	2203	4300	6503	SO:0001583	missense	10577	exon3			ACGGCCTTGCTGC	X67698	CCDS32121.1	14q24.3	2009-09-12				ENSG00000119655			14537	protein-coding gene	gene with protein product	"""epididymal protein 1"""	601015				8418812, 11125141	Standard	NM_006432		Approved	HE1, NP-C2, EDDM1	uc001xpy.3	P61916		ENST00000555619.1:c.212A>G	14.37:g.74951269T>C	ENSP00000451112:p.Lys71Arg	46.0	0.0	0		47.0	25.0	0.531915	NM_006432	B4DQV7|Q15668|Q29413	Missense_Mutation	SNP	ENST00000555619.1	37	CCDS32121.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	T|T	14.54|14.54	2.565104|2.565104	0.45694|0.45694	0.0|0.0	2.33E-4|2.33E-4	ENSG00000119655|ENSG00000119655	ENST00000434013;ENST00000541064;ENST00000555619;ENST00000238633;ENST00000553490;ENST00000557510;ENST00000555592|ENST00000556009	T;T;T;T;T;T;T|.	0.76968|.	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06|.	6.07|6.07	4.15|4.15	0.48705|0.48705	MD-2-related lipid-recognition (3);Immunoglobulin E-set (1);|.	0.381390|.	0.31010|.	N|.	0.008424|.	T|T	0.73048|0.73048	0.3537|0.3537	M|M	0.74546|0.74546	2.27|2.27	0.39428|0.39428	D|D	0.96703|0.96703	P;P|.	0.38677|.	0.642;0.642|.	P;B|.	0.46718|.	0.525;0.428|.	T|T	0.74121|0.74121	-0.3767|-0.3767	10|5	0.29301|.	T|.	0.29|.	-11.3591|-11.3591	14.5102|14.5102	0.67780|0.67780	0.0:0.0:0.4367:0.5633|0.0:0.0:0.4367:0.5633	.|.	71;71|.	B4DQV7;P61916|.	.;NPC2_HUMAN|.	R|G	71|93	ENSP00000412103:K71R;ENSP00000442488:K71R;ENSP00000451112:K71R;ENSP00000238633:K71R;ENSP00000451180:K71R;ENSP00000451206:K71R;ENSP00000450887:K71R|.	ENSP00000238633:K71R|.	K|R	-|-	2|1	0|2	NPC2|NPC2	74021022|74021022	0.865000|0.865000	0.29922|0.29922	0.886000|0.886000	0.34754|0.34754	0.099000|0.099000	0.18886|0.18886	1.204000|1.204000	0.32296|0.32296	0.771000|0.771000	0.33359|0.33359	0.533000|0.533000	0.62120|0.62120	AAG|AGG	T|1.000;C|0.000	0.000	strong		0.403	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432	
QRICH2	84074	hgsc.bcm.edu	37	17	74303550	74303550	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74303550G>A	ENST00000262765.5	-	1	211	c.32C>T	c.(31-33)gCc>gTc	p.A11V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	11										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GCTCACCCTGGCAAAGCTGAG	0.701																																					p.A11V		Atlas-SNP	.											.	QRICH2	143	.	0			c.C32T						PASS	.						56.0	51.0	53.0					17																	74303550		2203	4300	6503	SO:0001583	missense	84074	exon1			ACCCTGGCAAAGC	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.32C>T	17.37:g.74303550G>A	ENSP00000262765:p.Ala11Val	129.0	0.0	0		97.0	4.0	0.0412371	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	G	9.558	1.117648	0.20877	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08546	3.08	4.13	3.15	0.36227	.	.	.	.	.	T	0.05502	0.0145	N	0.14661	0.345	0.09310	N	1	B	0.29552	0.248	B	0.29077	0.098	T	0.38542	-0.9656	9	0.45353	T	0.12	11.3655	8.1866	0.31343	0.1154:0.0:0.8846:0.0	.	11	Q9H0J4	QRIC2_HUMAN	V	11	ENSP00000262765:A11V	ENSP00000262765:A11V	A	-	2	0	QRICH2	71815145	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.085000	0.14912	0.845000	0.35118	0.411000	0.27672	GCC	.	.	none		0.701	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ZNF311	282890	hgsc.bcm.edu	37	6	28963861	28963861	+	Silent	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:28963861G>C	ENST00000377179.3	-	7	1430	c.918C>G	c.(916-918)acC>acG	p.T306T	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	306					regulation of transcription, DNA-templated (GO:0006355)|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)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						TCCCACACTGGGTGCAATTAA	0.488																																					p.T306T		Atlas-SNP	.											.	ZNF311	59	.	0			c.C918G						PASS	.						81.0	82.0	82.0					6																	28963861		1510	2708	4218	SO:0001819	synonymous_variant	282890	exon7			ACACTGGGTGCAA	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.918C>G	6.37:g.28963861G>C		91.0	0.0	0		107.0	79.0	0.738318	NM_001010877	A2BFK5|B0S7Y4|Q92971	Silent	SNP	ENST00000377179.3	37	CCDS34357.1																																																																																			.	.	none		0.488	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
EPHA1	2041	hgsc.bcm.edu	37	7	143088584	143088584	+	Missense_Mutation	SNP	C	C	T	rs139482378	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143088584C>T	ENST00000275815.3	-	18	2983	c.2897G>A	c.(2896-2898)cGc>cAc	p.R966H	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	966	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GCAAAGAATGCGCTTCTGGTG	0.622													C|||	3	0.000599042	0.0008	0.0	5008	,	,		17063	0.0		0.002	False		,,,				2504	0.0				p.R966H		Atlas-SNP	.											EPHA1,NS,carcinoma,-1,1	EPHA1	193	1	0			c.G2897A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	95.0	61.0	72.0		2897	5.2	1.0	7	dbSNP_134	72	10,8590	8.4+/-32.0	0,10,4290	yes	missense	EPHA1	NM_005232.4	29	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	probably-damaging	966/977	143088584	10,12996	2203	4300	6503	SO:0001583	missense	2041	exon18			AGAATGCGCTTCT	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.2897G>A	7.37:g.143088584C>T	ENSP00000275815:p.Arg966His	121.0	0.0	0		104.0	52.0	0.5	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	25.0	4.594043	0.86953	0.0	0.001163	ENSG00000146904	ENST00000275815	T	0.55052	0.54	5.24	5.24	0.73138	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.56097	D	0.000029	T	0.77274	0.4106	M	0.92555	3.32	0.53005	D	0.999961	D	0.89917	1.0	D	0.79784	0.993	T	0.82014	-0.0667	10	0.87932	D	0	.	12.3566	0.55178	0.0:0.9237:0.0:0.0763	.	966	P21709	EPHA1_HUMAN	H	966	ENSP00000275815:R966H	ENSP00000275815:R966H	R	-	2	0	EPHA1	142798706	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.577000	0.46042	2.724000	0.93272	0.561000	0.74099	CGC	C|0.999;T|0.001	0.001	strong		0.622	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
MUC4	4585	hgsc.bcm.edu	37	3	195505746	195505746	+	Silent	SNP	T	T	G	rs369426870		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505746T>G	ENST00000463781.3	-	2	13164	c.12705A>C	c.(12703-12705)acA>acC	p.T4235T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4235T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	992					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGCGTGACCTGTGGATACTG	0.587																																					p.T4235T		Atlas-SNP	.											.	MUC4	1505	.	0			c.A12705C						PASS	.	T	,,	12,4206		0,12,2097	48.0	48.0	48.0		,12705,	2.3	0.3	3		48	120,8280		1,118,4081	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	1,130,6178	GG,GT,TT		1.4286,0.2845,1.0461	,,	,4235/5413,	195505746	132,12486	2109	4200	6309	SO:0001819	synonymous_variant	4585	exon2			GTGACCTGTGGAT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12705A>C	3.37:g.195505746T>G		90.0	0.0	0		70.0	21.0	0.3	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	3.587	-0.084433	0.07097	0.002845	0.014286	ENSG00000145113	ENST00000392409	.	.	.	2.31	2.31	0.28768	.	.	.	.	.	.	.	.	.	.	.	0.25916	N	0.983177	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.531	0.22326	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MUC4	196990525	0.008000	0.16893	0.260000	0.24451	0.033000	0.12548	0.285000	0.18883	1.300000	0.44818	0.482000	0.46254	.	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107302	27107302	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27107302C>G	ENST00000354348.2	+	1	227	c.215C>G	c.(214-216)aCc>aGc	p.T72S	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	72					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(1)	1						GACGCCGTGACCTACACGGAG	0.642			T	BCL6	NHL																																p.T72S		Atlas-SNP	.		Dom	yes		6	6p21.3	8294	"""histone 1, H4i (H4FM)"""		L	.	HIST1H4I	26	.	0			c.C215G						PASS	.						77.0	69.0	72.0					6																	27107302		2203	4300	6503	SO:0001583	missense	8294	exon1			CCGTGACCTACAC	AB000905	CCDS4620.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198339	ENSG00000276180		"""Histones / Replication-dependent"""	4793	protein-coding gene	gene with protein product		602833	"""H4 histone family, member M"", ""histone 1, H4i"""	H4FM		8988030, 9439656, 12408966	Standard	NM_003495		Approved	H4/m	uc003niy.1	P62805	OTTHUMG00000014471	ENST00000354348.2:c.215C>G	6.37:g.27107302C>G	ENSP00000346316:p.Thr72Ser	116.0	0.0	0		141.0	93.0	0.659574	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000354348.2	37	CCDS4620.1	.	.	.	.	.	.	.	.	.	.	.	22.7	4.318985	0.81469	.	.	ENSG00000198339	ENST00000354348	T	0.67523	-0.27	3.8	3.8	0.43715	.	0.000000	0.41605	U	0.000849	T	0.75221	0.3820	M	0.82823	2.61	0.50313	D	0.999864	.	.	.	.	.	.	T	0.80155	-0.1500	8	0.72032	D	0.01	.	13.9996	0.64424	0.0:1.0:0.0:0.0	.	.	.	.	S	72	ENSP00000346316:T72S	ENSP00000346316:T72S	T	+	2	0	HIST1H4I	27215281	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.052000	0.76634	2.068000	0.61886	0.655000	0.94253	ACC	.	.	none		0.642	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495	
DCANP1	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782443T>C	ENST00000503143.2	-	1	595	c.356A>G	c.(355-357)aAg>aGg	p.K119R	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		119						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGGCCTGTCTTCCTTCTGCT	0.547													T|||	452	0.0902556	0.3033	0.0418	5008	,	,		19866	0.0		0.0179	False		,,,				2504	0.0041				p.K119R		Atlas-SNP	.											.	C5orf20	16	.	0			c.A356G						PASS	.	T	ARG/LYS	1160,3246	410.9+/-335.5	154,852,1197	112.0	120.0	117.0		356	0.2	0.0	5	dbSNP_132	117	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	26	155,969,5379	CC,CT,TT		1.3837,26.3277,9.8339	benign	119/245	134782443	1279,11727	2203	4300	6503	SO:0001583	missense	140947	exon1			CCTGTCTTCCTTC																												ENST00000503143.2:c.356A>G	5.37:g.134782443T>C	ENSP00000421871:p.Lys119Arg	65.0	0.0	0		58.0	24.0	0.413793	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	170	0.07783882783882784	139	0.28252032520325204	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	5.813	0.334340	0.11013	0.263277	0.013837	ENSG00000251380	ENST00000503143	T	0.37915	1.17	2.78	0.236	0.15471	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.16603	0.018	B	0.08055	0.003	T	0.36089	-0.9762	8	0.87932	D	0	.	3.1238	0.06400	0.5045:0.2511:0.0:0.2444	.	119	Q8TF63	DCNP1_HUMAN	R	119	ENSP00000421871:K119R	ENSP00000421871:K119R	K	-	2	0	C5orf20	134810342	0.000000	0.05858	0.013000	0.15412	0.047000	0.14425	-0.373000	0.07494	0.043000	0.15746	-0.669000	0.03829	AAG	T|0.902;C|0.098	0.098	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs544842497|rs2259820	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121435342C>T	ENST00000257555.6	+	7	1601	c.1375C>T	c.(1375-1377)Ctg>Ttg	p.L459L	HNF1A_ENST00000538626.1_Silent_p.L41L|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L			P20823	HNF1A_HUMAN	HNF1 homeobox A	459					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTGACCACCCTGCAGCCCGT	0.667									Hepatic Adenoma, Familial Clustering of				c|||	1586	0.316693	0.1089	0.3501	5008	,	,		17758	0.4732		0.3161	False		,,,				2504	0.4131				p.L459L		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1375T						PASS	.	C		529,3877	232.0+/-245.7	41,447,1715	33.0	35.0	34.0		1375	4.6	1.0	12	dbSNP_100	34	2675,5923	412.6+/-350.9	434,1807,2058	no	coding-synonymous	HNF1A	NM_000545.5		475,2254,3773	TT,TC,CC		31.1119,12.0064,24.6386		459/632	121435342	3204,9800	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCACCCTGCAGC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1375C>T	12.37:g.121435342C>T		70.0	0.0	0		117.0	116.0	0.991453	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			C|0.718;T|0.282	0.282	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
CRISPLD2	83716	hgsc.bcm.edu	37	16	84900645	84900645	+	Splice_Site	SNP	G	G	A	rs149615348	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84900645G>A	ENST00000262424.5	+	7	1076	c.852G>A	c.(850-852)atG>atA	p.M284I	CRISPLD2_ENST00000567845.1_Splice_Site_p.M283I|CRISPLD2_ENST00000564567.1_Splice_Site_p.M284I	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	284	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						TCAACTACATGAGTGAGTCTA	0.582													G|||	13	0.00259585	0.0008	0.0058	5008	,	,		15855	0.0		0.007	False		,,,				2504	0.001				p.M284I		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.G852A						PASS	.	G	ILE/MET	7,4391	12.9+/-30.5	0,7,2192	98.0	86.0	90.0		852	5.4	1.0	16	dbSNP_134	90	67,8533	41.2+/-98.3	1,65,4234	yes	missense-near-splice	CRISPLD2	NM_031476.3	10	1,72,6426	AA,AG,GG		0.7791,0.1592,0.5693	benign	284/498	84900645	74,12924	2199	4300	6499	SO:0001630	splice_region_variant	83716	exon7			CTACATGAGTGAG	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.853+1G>A	16.37:g.84900645G>A		79.0	0.0	0		54.0	24.0	0.444444	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	15.98	2.991514	0.54041	0.001592	0.007791	ENSG00000103196	ENST00000262424	D	0.88818	-2.43	5.36	5.36	0.76844	LCCL (3);	0.291378	0.41938	D	0.000792	D	0.85687	0.5754	M	0.71581	2.175	0.80722	D	1	B;B;B	0.28933	0.179;0.019;0.228	B;B;B	0.30855	0.084;0.013;0.121	D	0.86000	0.1494	10	0.51188	T	0.08	.	16.5865	0.84728	0.0:0.0:1.0:0.0	.	284;284;284	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	I	284	ENSP00000262424:M284I	ENSP00000262424:M284I	M	+	3	0	CRISPLD2	83458146	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.753000	0.68736	2.514000	0.84764	0.561000	0.74099	ATG	G|0.994;A|0.006	0.006	strong		0.582	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	Missense_Mutation
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38537579T>C	ENST00000378954.4	-	8	816	c.815A>G	c.(814-816)aAt>aGt	p.N272S	ATL2_ENST00000419554.2_Missense_Mutation_p.N272S|ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000452935.2_Missense_Mutation_p.N254S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	272	GB1/RHD3-type G.		N -> S (in dbSNP:rs34873284).		endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						TTCATGTTGATTTTGTTTTAC	0.383													T|||	72	0.014377	0.0045	0.0216	5008	,	,		17843	0.0		0.0398	False		,,,				2504	0.0112				p.N272S		Atlas-SNP	.											.	ATL2	49	.	0			c.A815G						PASS	.	T	SER/ASN,SER/ASN	48,4358	48.9+/-83.8	1,46,2156	133.0	118.0	123.0		815,815	5.1	1.0	2	dbSNP_126	123	420,8180	130.8+/-188.7	10,400,3890	yes	missense,missense	ATL2	NM_001135673.1,NM_022374.2	46,46	11,446,6046	CC,CT,TT		4.8837,1.0894,3.5983	benign,benign	272/584,272/580	38537579	468,12538	2203	4300	6503	SO:0001583	missense	64225	exon8			TGTTGATTTTGTT		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.815A>G	2.37:g.38537579T>C	ENSP00000368237:p.Asn272Ser	107.0	0.0	0		97.0	58.0	0.597938	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	40|40	0.018315018315018316|0.018315018315018316	4|4	0.008130081300813009|0.008130081300813009	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	T|T	15.82|15.82	2.945674|2.945674	0.53079|0.53079	0.010894|0.010894	0.048837|0.048837	ENSG00000119787|ENSG00000119787	ENST00000443098|ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130	.|T;T;T;T;T;T;T;T;T	.|0.74421	.|-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Guanylate-binding protein, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28764|0.28764	0.0713|0.0713	L|L	0.47078|0.47078	1.49|1.49	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.17268	.|0.021;0.001;0.003;0.005;0.001	.|B;B;B;B;B	.|0.11329	.|0.006;0.001;0.001;0.002;0.002	T|T	0.53542|0.53542	-0.8424|-0.8424	5|10	.|0.44086	.|T	.|0.13	-21.5939|-21.5939	14.0983|14.0983	0.65037|0.65037	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34873284;rs61754250|rs34873284;rs61754250	.|101;254;254;272;272	.|B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.|.;.;.;.;ATLA2_HUMAN	V|S	191|272;101;101;101;254;272;254;101;90	.|ENSP00000368237:N272S;ENSP00000385446:N101S;ENSP00000384062:N101S;ENSP00000446192:N101S;ENSP00000333393:N254S;ENSP00000415336:N272S;ENSP00000390743:N254S;ENSP00000438938:N101S;ENSP00000409811:N90S	.|ENSP00000333393:N254S	I|N	-|-	1|2	0|0	ATL2|ATL2	38391083|38391083	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.982000|0.982000	0.71751|0.71751	6.134000|6.134000	0.71689|0.71689	1.917000|1.917000	0.55516|0.55516	0.455000|0.455000	0.32223|0.32223	ATC|AAT	T|0.967;C|0.033	0.033	strong		0.383	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
KLHDC4	54758	hgsc.bcm.edu	37	16	87782322	87782322	+	Missense_Mutation	SNP	G	G	C	rs3751727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:87782322G>C	ENST00000270583.5	-	5	521	c.463C>G	c.(463-465)Ctc>Gtc	p.L155V	KLHDC4_ENST00000347925.5_Missense_Mutation_p.L155V|RP11-278A23.2_ENST00000563036.1_RNA|KLHDC4_ENST00000353170.5_Missense_Mutation_p.L98V	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	155			L -> V (in dbSNP:rs3751727).							breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGACCCAGAGATCCTTGTAG	0.557													G|||	128	0.0255591	0.0121	0.0101	5008	,	,		19581	0.0546		0.0278	False		,,,				2504	0.0225				p.L155V		Atlas-SNP	.											.	KLHDC4	45	.	0			c.C463G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU	59,4337	57.4+/-93.9	0,59,2139	177.0	175.0	175.0		292,463,463	5.0	1.0	16	dbSNP_107	175	249,8351	97.7+/-159.3	6,237,4057	yes	missense,missense,missense	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	32,32,32	6,296,6196	CC,CG,GG		2.8953,1.3421,2.37	possibly-damaging,possibly-damaging,possibly-damaging	98/464,155/490,155/521	87782322	308,12688	2198	4300	6498	SO:0001583	missense	54758	exon5			CCCAGAGATCCTT	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.463C>G	16.37:g.87782322G>C	ENSP00000270583:p.Leu155Val	51.0	0.0	0		70.0	28.0	0.4	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	58	0.026556776556776556	5	0.01016260162601626	1	0.0027624309392265192	32	0.055944055944055944	20	0.026385224274406333	G	25.5	4.645314	0.87859	0.013421	0.028953	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.62232	0.04;0.04;0.04	4.97	4.97	0.65823	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.34366	0.0895	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	0.992;1.0;0.999	D;D;D	0.80764	0.976;0.994;0.988	T	0.64782	-0.6326	10	0.46703	T	0.11	0.8402	17.5767	0.87952	0.0:0.0:1.0:0.0	rs3751727;rs17699822;rs52805401;rs3751727	98;155;155	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	V	155;155;98	ENSP00000270583:L155V;ENSP00000325717:L155V;ENSP00000262530:L98V	ENSP00000270583:L155V	L	-	1	0	KLHDC4	86339823	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.891000	0.92485	2.450000	0.82876	0.561000	0.74099	CTC	G|0.974;C|0.026	0.026	strong		0.557	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566	
MYH13	8735	hgsc.bcm.edu	37	17	10222310	10222310	+	Missense_Mutation	SNP	G	G	A	rs200861648	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10222310G>A	ENST00000418404.3	-	26	3698	c.3535C>T	c.(3535-3537)Cgc>Tgc	p.R1179C	MYH13_ENST00000252172.4_Missense_Mutation_p.R1179C|RP11-401O9.4_ENST00000609088.1_RNA|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1179					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						AGGTCCCTGCGCATTTTCTGG	0.582													G|||	2	0.000399361	0.0	0.0014	5008	,	,		17738	0.0		0.001	False		,,,				2504	0.0				p.R1179C		Atlas-SNP	.											MYH13_ENST00000252172,right_upper_lobe,carcinoma,0,2	MYH13	533	2	0			c.C3535T						PASS	.	G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	132.0	135.0	134.0		3535	4.1	1.0	17	dbSNP_132	134	6,8594	5.0+/-18.6	0,6,4294	no	missense	MYH13	NM_003802.2	180	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	probably-damaging	1179/1939	10222310	8,12998	2203	4300	6503	SO:0001583	missense	8735	exon27			CCCTGCGCATTTT	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3535C>T	17.37:g.10222310G>A	ENSP00000404570:p.Arg1179Cys	155.0	0.0	0		138.0	56.0	0.405797	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.64	3.438775	0.62955	4.54E-4	6.98E-4	ENSG00000006788	ENST00000252172	D	0.84070	-1.8	4.05	4.05	0.47172	Myosin tail (1);	.	.	.	.	D	0.93867	0.8038	H	0.97983	4.12	0.44862	D	0.997876	D	0.89917	1.0	D	0.97110	1.0	D	0.95113	0.8240	9	0.87932	D	0	.	11.9523	0.52962	0.0:0.0:0.8264:0.1735	.	1179	Q9UKX3	MYH13_HUMAN	C	1179	ENSP00000252172:R1179C	ENSP00000252172:R1179C	R	-	1	0	MYH13	10163035	1.000000	0.71417	0.972000	0.41901	0.989000	0.77384	4.380000	0.59581	2.236000	0.73375	0.591000	0.81541	CGC	G|1.000;A|0.000	0.000	strong		0.582	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
CCDC158	339965	hgsc.bcm.edu	37	4	77255210	77255210	+	Silent	SNP	C	C	T	rs113022439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:77255210C>T	ENST00000388914.3	-	18	2927	c.2775G>A	c.(2773-2775)aaG>aaA	p.K925K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	925										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						CTTCCTCTGTCTTGCTCAGAG	0.483													C|||	32	0.00638978	0.0015	0.0072	5008	,	,		17210	0.0		0.0239	False		,,,				2504	0.001				p.K925K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2775A						PASS	.	C		15,4101		0,15,2043	158.0	159.0	159.0		2775	3.8	0.6	4	dbSNP_132	159	300,8128		4,292,3918	no	coding-synonymous	CCDC158	NM_001042784.1		4,307,5961	TT,TC,CC		3.5596,0.3644,2.5112		925/1114	77255210	315,12229	2058	4214	6272	SO:0001819	synonymous_variant	339965	exon18			CTCTGTCTTGCTC	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2775G>A	4.37:g.77255210C>T		138.0	0.0	0		140.0	140.0	1	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			C|0.984;T|0.016	0.016	strong		0.483	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
HMBOX1	79618	hgsc.bcm.edu	37	8	28827928	28827928	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:28827928A>T	ENST00000397358.3	+	4	1096	c.392A>T	c.(391-393)aAg>aTg	p.K131M	HMBOX1_ENST00000355231.5_Missense_Mutation_p.K131M|HMBOX1_ENST00000524238.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000403668.2_Missense_Mutation_p.K131M|HMBOX1_ENST00000519047.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000523613.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000287701.10_Missense_Mutation_p.K131M|HMBOX1_ENST00000444075.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000558662.1_Missense_Mutation_p.K131M	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	131					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	11		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		TCCAATGGAAAGATGTCACCA	0.448																																					p.K131M		Atlas-SNP	.											.	HMBOX1	34	.	0			c.A392T						PASS	.						78.0	76.0	77.0					8																	28827928		2203	4300	6503	SO:0001583	missense	79618	exon4			ATGGAAAGATGTC	AY522342	CCDS6071.1	8p12	2013-05-23			ENSG00000147421	ENSG00000147421		"""Homeoboxes / HNF class"""	26137	protein-coding gene	gene with protein product	"""homeobox telomere-binding protein 1"""					16825764	Standard	NM_024567		Approved	HNF1LA, PBHNF, FLJ21616, HOT1	uc003xhd.4	Q6NT76	OTTHUMG00000172138	ENST00000397358.3:c.392A>T	8.37:g.28827928A>T	ENSP00000380516:p.Lys131Met	52.0	0.0	0		87.0	4.0	0.045977	NM_024567	A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Missense_Mutation	SNP	ENST00000397358.3	37	CCDS6071.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453485	0.84209	.	.	ENSG00000147421	ENST00000287701;ENST00000444075;ENST00000403668;ENST00000519047;ENST00000397358;ENST00000524238;ENST00000517340;ENST00000355231	D;D;D;D;D;D	0.98474	-4.95;-4.95;-4.95;-4.95;-4.95;-4.95	5.88	5.88	0.94601	Hepatocyte nuclear factor 1, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98435	0.9479	L	0.51422	1.61	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.997;0.997;0.997;0.998;0.998	D	0.99764	1.1022	10	0.54805	T	0.06	-12.0241	16.2965	0.82776	1.0:0.0:0.0:0.0	.	131;131;131;131;131;131	Q6NT76-5;D3DSU2;Q6NT76-2;Q6NT76-3;Q6NT76;E5RGZ2	.;.;.;.;HMBX1_HUMAN;.	M	131	ENSP00000287701:K131M;ENSP00000401769:K131M;ENSP00000384261:K131M;ENSP00000430059:K131M;ENSP00000380516:K131M;ENSP00000430110:K131M	ENSP00000287701:K131M	K	+	2	0	HMBOX1	28883847	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.818000	0.91991	2.243000	0.73865	0.528000	0.53228	AAG	.	.	none		0.448	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255267.4	NM_024567	
TFDP3	51270	hgsc.bcm.edu	37	X	132351703	132351703	+	Missense_Mutation	SNP	C	C	A	rs35745873	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:132351703C>A	ENST00000310125.4	-	1	673	c.585G>T	c.(583-585)caG>caT	p.Q195H		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	195	Involved in negatively regulating E2F activity.				cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					TCTGACAGTTCTGAGCCGAGT	0.438													C|||	85	0.0225166	0.0098	0.0187	3775	,	,		16569	0.002		0.0288	False		,,,				2504	0.0286				p.Q195H		Atlas-SNP	.											.	TFDP3	92	.	0			c.G585T						PASS	.	C	HIS/GLN	36,3799		0,29,7,1603,564	104.0	97.0	99.0		585	0.2	0.0	X	dbSNP_126	99	262,6466		3,197,59,2228,1813	yes	missense	TFDP3	NM_016521.2	24	3,226,66,3831,2377	AA,AC,A,CC,C		3.8942,0.9387,2.8212	probably-damaging	195/406	132351703	298,10265	2203	4300	6503	SO:0001583	missense	51270	exon1			ACAGTTCTGAGCC	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.585G>T	X.37:g.132351703C>A	ENSP00000385461:p.Gln195His	71.0	0.0	0		84.0	28.0	0.333333	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	43	0.02591922845087402	5	0.010245901639344262	6	0.01675977653631285	2	0.0034965034965034965	14	0.01907356948228883	c	11.08	1.534355	0.27475	0.009387	0.038942	ENSG00000183434	ENST00000310125	T	0.27104	1.69	0.208	0.208	0.15221	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor DP, C-terminal (1);	.	.	.	.	T	0.13628	0.0330	M	0.83774	2.66	0.09310	P	0.9999988559	P	0.46142	0.873	P	0.55087	0.768	T	0.41998	-0.9477	8	0.87932	D	0	.	6.1509	0.20310	0.0:0.9996:0.0:4.0E-4	rs35745873;rs35745873	195	Q5H9I0	TFDP3_HUMAN	H	195	ENSP00000385461:Q195H	ENSP00000385461:Q195H	Q	-	3	2	TFDP3	132179369	0.998000	0.40836	0.018000	0.16275	0.019000	0.09904	0.277000	0.18734	0.268000	0.21939	0.271000	0.19318	CAG	C|0.978;A|0.022	0.022	strong		0.438	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
KEAP1	9817	hgsc.bcm.edu	37	19	10602344	10602344	+	Missense_Mutation	SNP	G	G	A	rs147613351		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10602344G>A	ENST00000171111.5	-	3	1781	c.1234C>T	c.(1234-1236)Ccc>Tcc	p.P412S	KEAP1_ENST00000588024.1_5'Flank|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Missense_Mutation_p.P412S	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	412					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CGGTTACGGGGCACGCTCATG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15649	0.0		0.001	False		,,,				2504	0.0				p.P412S		Atlas-SNP	.											.	KEAP1	182	.	0			c.C1234T						PASS	.	G	SER/PRO,SER/PRO	0,4402		0,0,2201	34.0	29.0	31.0		1234,1234	5.6	1.0	19	dbSNP_134	31	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	KEAP1	NM_012289.3,NM_203500.1	74,74	0,5,6496	AA,AG,GG		0.0581,0.0,0.0385	probably-damaging,probably-damaging	412/625,412/625	10602344	5,12997	2201	4300	6501	SO:0001583	missense	9817	exon3			TACGGGGCACGCT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1234C>T	19.37:g.10602344G>A	ENSP00000171111:p.Pro412Ser	115.0	0.0	0		98.0	43.0	0.438776	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	37	CCDS12239.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	14.70	2.612736	0.46631	0.0	5.81E-4	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.79749	-1.3;-1.3	5.6	5.6	0.85130	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.88336	0.6409	M	0.66297	2.02	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.87234	0.2262	10	0.41790	T	0.15	.	17.1192	0.86697	0.0:0.0:1.0:0.0	.	412	Q14145	KEAP1_HUMAN	S	412	ENSP00000171111:P412S;ENSP00000377245:P412S	ENSP00000171111:P412S	P	-	1	0	KEAP1	10463344	1.000000	0.71417	0.955000	0.39395	0.717000	0.41224	4.656000	0.61483	2.662000	0.90505	0.655000	0.94253	CCC	G|1.000;A|0.000	0.000	strong		0.652	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
PRSS3	5646	hgsc.bcm.edu	37	9	33799103	33799103	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33799103G>A	ENST00000361005.5	+	5	840	c.840G>A	c.(838-840)aaG>aaA	p.K280K	PRSS3_ENST00000342836.4_Silent_p.K237K|PRSS3_ENST00000429677.3_Silent_p.K216K|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000495682.1_3'UTR|PRSS3_ENST00000379405.3_Silent_p.K223K	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	280	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GTGCCTGGAAGAACAGGCCTG	0.572																																					p.K280K		Atlas-SNP	.											.	PRSS3	79	.	0			c.G840A						PASS	.						95.0	91.0	92.0					9																	33799103		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon5			CTGGAAGAACAGG		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.840G>A	9.37:g.33799103G>A		176.0	0.0	0		210.0	9.0	0.0428571	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.	.	none		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
ZNF469	84627	hgsc.bcm.edu	37	16	88500957	88500957	+	Missense_Mutation	SNP	C	C	T	rs76389306	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88500957C>T	ENST00000437464.1	+	2	6995	c.6995C>T	c.(6994-6996)cCg>cTg	p.P2332L	ZNF469_ENST00000565624.1_Missense_Mutation_p.P2360L	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2332					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GGTGCAGGGCCGGACTCCCCC	0.667													C|||	7	0.00139776	0.0	0.0029	5008	,	,		15359	0.0		0.005	False		,,,				2504	0.0				p.P2332L		Atlas-SNP	.											.	ZNF469	121	.	0			c.C6995T						PASS	.						8.0	13.0	11.0					16																	88500957		687	1578	2265	SO:0001583	missense	84627	exon2			CAGGGCCGGACTC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.6995C>T	16.37:g.88500957C>T	ENSP00000402343:p.Pro2332Leu	74.0	0.0	0		74.0	35.0	0.472973	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	6.919	0.539181	0.13250	.	.	ENSG00000225614	ENST00000437464	T	0.47177	0.85	3.9	0.555	0.17247	.	.	.	.	.	T	0.18341	0.0440	N	0.12182	0.205	0.09310	N	1	B	0.20550	0.046	B	0.13407	0.009	T	0.18272	-1.0342	9	0.72032	D	0.01	.	3.4603	0.07531	0.0:0.532:0.2154:0.2526	.	2332	Q96JG9	ZN469_HUMAN	L	2332	ENSP00000402343:P2332L	ENSP00000402343:P2332L	P	+	2	0	ZNF469	87028458	0.000000	0.05858	0.021000	0.16686	0.002000	0.02628	0.061000	0.14366	0.764000	0.33197	-0.657000	0.03884	CCG	C|0.998;T|0.002	0.002	strong		0.667	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MSGN1	343930	hgsc.bcm.edu	37	2	17998001	17998001	+	Silent	SNP	C	C	T	rs201149255	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:17998001C>T	ENST00000281047.3	+	1	239	c.216C>T	c.(214-216)ggC>ggT	p.G72G		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	72					cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTGAGCACGGCGGGGCCAGCA	0.627													C|||	3	0.000599042	0.0	0.0	5008	,	,		17091	0.0		0.002	False		,,,				2504	0.001				p.G72G	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											MSGN1,NS,carcinoma,+1,1	MSGN1	39	1	0			c.C216T						PASS	.	C		4,3852		0,4,1924	39.0	46.0	44.0		216	-10.2	0.0	2		44	21,8207		0,21,4093	no	coding-synonymous	MSGN1	NM_001105569.1		0,25,6017	TT,TC,CC		0.2552,0.1037,0.2069		72/194	17998001	25,12059	1928	4114	6042	SO:0001819	synonymous_variant	343930	exon1			GCACGGCGGGGCC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.216C>T	2.37:g.17998001C>T		67.0	0.0	0		77.0	33.0	0.428571	NM_001105569		Silent	SNP	ENST00000281047.3	37	CCDS42657.1																																																																																			C|0.999;T|0.001	0.001	strong		0.627	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
DUSP8	1850	hgsc.bcm.edu	37	11	1580173	1580173	+	Silent	SNP	C	C	A	rs17854342		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1580173C>A	ENST00000397374.3	-	4	610	c.483G>T	c.(481-483)ctG>ctT	p.L161L	DUSP8_ENST00000331588.4_Silent_p.L161L|DUSP8_ENST00000528778.1_5'UTR	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	161					inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|lung(2)|prostate(1)|urinary_tract(1)	5		all_epithelial(84;0.000134)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000621)|Lung(200;0.0687)|LUSC - Lung squamous cell carcinoma(625;0.0825)		GGATGCGGGTCAGGCCCACGC	0.652																																					p.L161L		Atlas-SNP	.											.	DUSP8	22	.	0			c.G483T						PASS	.						91.0	76.0	81.0					11																	1580173		2202	4299	6501	SO:0001819	synonymous_variant	1850	exon4			GCGGGTCAGGCCC		CCDS7724.1	11p15.5	2011-06-09			ENSG00000184545	ENSG00000184545		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3074	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""H1 phosphatase, vaccinia virus homolog"""	602038	"""chromosome 11 open reading frame 81"""	C11orf81		7561881, 9192849	Standard	NM_004420		Approved	HVH-5, HB5, FLJ42958	uc001lts.2	Q13202	OTTHUMG00000133348	ENST00000397374.3:c.483G>T	11.37:g.1580173C>A		119.0	0.0	0		119.0	34.0	0.285714	NM_004420	Q86SS8	Silent	SNP	ENST00000397374.3	37	CCDS7724.1																																																																																			.	.	alt		0.652	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420	
MROH1	727957	hgsc.bcm.edu	37	8	145223239	145223239	+	Missense_Mutation	SNP	C	C	T	rs374952645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145223239C>T	ENST00000528919.1	+	3	185	c.64C>T	c.(64-66)Ccc>Tcc	p.P22S	MROH1_ENST00000326134.5_Missense_Mutation_p.P22S|MROH1_ENST00000423230.2_Missense_Mutation_p.P22S|MROH1_ENST00000534366.1_Missense_Mutation_p.P22S|MROH1_ENST00000398656.4_Missense_Mutation_p.P22S	NM_032450.2	NP_115826	Q8NDA8	MROH1_HUMAN	maestro heat-like repeat family member 1	22																	CGATAAGGACCCCCTGGTGCA	0.657																																					p.P22S		Atlas-SNP	.											.	.	.	.	0			c.C64T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	1,4221		0,1,2110	29.0	33.0	32.0		64,64,64	5.2	1.0	8		32	0,8440		0,0,4220	no	missense,missense,missense	HEATR7A	NM_001099280.1,NM_001099281.1,NM_032450.2	74,74,74	0,1,6330	TT,TC,CC		0.0,0.0237,0.0079	benign,benign,benign	22/423,22/423,22/1642	145223239	1,12661	2111	4220	6331	SO:0001583	missense	727957	exon4			AAGGACCCCCTGG		CCDS47938.1, CCDS47939.1, CCDS75803.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000179832	ENSG00000179832		"""maestro heat-like repeat containing"""	26958	protein-coding gene	gene with protein product			"""HEAT repeat containing 7A"""	HEATR7A		11347906	Standard	NM_032450		Approved	KIAA1833	uc003zbk.4	Q8NDA8	OTTHUMG00000165781	ENST00000528919.1:c.64C>T	8.37:g.145223239C>T	ENSP00000435565:p.Pro22Ser	31.0	0.0	0		36.0	9.0	0.25	NM_001099280	C9JWM5|D3DWL5|Q0P612|Q569G6|Q6NVW4|Q8N230|Q8NAD1|Q8ND95|Q96JJ4	Missense_Mutation	SNP	ENST00000528919.1	37	CCDS47938.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108333	0.37242	2.37E-4	0.0	ENSG00000179832	ENST00000423230;ENST00000398656;ENST00000534366;ENST00000528919;ENST00000326134	T;T;T;T;T	0.68624	-0.27;-0.34;-0.34;-0.34;-0.34	5.18	5.18	0.71444	Armadillo-like helical (1);Armadillo-type fold (1);	0.420102	0.19324	U	0.117043	T	0.68869	0.3048	M	0.61703	1.905	0.80722	D	1	B;D;D;B;B	0.54047	0.098;0.964;0.964;0.199;0.2	B;P;P;B;B	0.49140	0.031;0.601;0.601;0.067;0.047	T	0.64715	-0.6342	10	0.10636	T	0.68	.	16.5435	0.84408	0.0:1.0:0.0:0.0	.	22;22;22;22;22	Q8NDA8-2;E9PHY8;Q8NDA8;Q8NDA8-4;Q8NDA8-5	.;.;HTR7A_HUMAN;.;.	S	22	ENSP00000388174:P22S;ENSP00000381649:P22S;ENSP00000436636:P22S;ENSP00000435565:P22S;ENSP00000321737:P22S	ENSP00000321737:P22S	P	+	1	0	HEATR7A	145295227	0.186000	0.23225	0.981000	0.43875	0.443000	0.32047	2.161000	0.42358	2.582000	0.87167	0.563000	0.77884	CCC	.	.	weak		0.657	MROH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386183.1	NM_032450	
CLRN3	119467	hgsc.bcm.edu	37	10	129690837	129690837	+	Missense_Mutation	SNP	G	G	T	rs35890579	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129690837G>T	ENST00000368671.3	-	1	374	c.212C>A	c.(211-213)cCa>cAa	p.P71Q		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	71						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				CTTTTTCTTTGGTTCTGCAAG	0.358													G|||	75	0.014976	0.0023	0.0159	5008	,	,		18682	0.0		0.0467	False		,,,				2504	0.0143				p.P71Q		Atlas-SNP	.											.	CLRN3	27	.	0			c.C212A						PASS	.	G	GLN/PRO	37,4369	41.6+/-74.8	0,37,2166	84.0	81.0	82.0		212	3.0	0.0	10	dbSNP_126	82	441,8159	132.3+/-190.0	15,411,3874	yes	missense	CLRN3	NM_152311.3	76	15,448,6040	TT,TG,GG		5.1279,0.8398,3.6752	benign	71/227	129690837	478,12528	2203	4300	6503	SO:0001583	missense	119467	exon1			TTCTTTGGTTCTG	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.212C>A	10.37:g.129690837G>T	ENSP00000357660:p.Pro71Gln	50.0	0.0	0		79.0	38.0	0.481013	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	45	0.020604395604395604	3	0.006097560975609756	8	0.022099447513812154	0	0.0	34	0.044854881266490766	G	9.541	1.113346	0.20795	0.008398	0.051279	ENSG00000180745	ENST00000368671	T	0.75589	-0.95	5.52	2.96	0.34315	.	1.135500	0.06413	N	0.721034	T	0.27967	0.0689	L	0.36672	1.1	0.09310	N	1	P	0.43542	0.81	P	0.45998	0.5	T	0.31696	-0.9934	10	0.12430	T	0.62	.	6.9764	0.24677	0.2997:0.0:0.7003:0.0	rs35890579	71	Q8NCR9	CLRN3_HUMAN	Q	71	ENSP00000357660:P71Q	ENSP00000357660:P71Q	P	-	2	0	CLRN3	129580827	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.299000	0.19138	0.460000	0.27045	0.655000	0.94253	CCA	G|0.966;T|0.034	0.034	strong		0.358	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
PKP3	11187	hgsc.bcm.edu	37	11	403658	403658	+	Missense_Mutation	SNP	G	G	C	rs147657735		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:403658G>C	ENST00000331563.2	+	10	2040	c.1964G>C	c.(1963-1965)cGt>cCt	p.R655P		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	655					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCAGGAGCGTATTCTGAAC	0.667													g|||	1	0.000199681	0.0	0.0	5008	,	,		16683	0.0		0.001	False		,,,				2504	0.0				p.R655P		Atlas-SNP	.											PKP3,NS,lymphoid_neoplasm,0,1	PKP3	36	1	0			c.G1964C						PASS	.		PRO/ARG	5,4357	9.9+/-24.2	0,5,2176	68.0	60.0	62.0		1964	3.8	1.0	11	dbSNP_134	62	10,8556	7.7+/-29.5	0,10,4273	yes	missense	PKP3	NM_007183.2	103	0,15,6449	CC,CG,GG		0.1167,0.1146,0.116	probably-damaging	655/798	403658	15,12913	2181	4283	6464	SO:0001583	missense	11187	exon10			AGGAGCGTATTCT	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"""Armadillo repeat containing"""	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.1964G>C	11.37:g.403658G>C	ENSP00000331678:p.Arg655Pro	26.0	0.0	0		28.0	17.0	0.607143	NM_007183	F8J390|Q53EX8	Missense_Mutation	SNP	ENST00000331563.2	37	CCDS7695.1	.	.	.	.	.	.	.	.	.	.	g	17.63	3.436167	0.62955	0.001146	0.001167	ENSG00000184363	ENST00000331563	T	0.48201	0.82	3.85	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	0.088251	0.50627	D	0.000102	T	0.66781	0.2824	M	0.66939	2.045	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.72567	-0.4254	10	0.87932	D	0	-16.9262	16.3352	0.83056	0.0:0.0:1.0:0.0	.	655	Q9Y446	PKP3_HUMAN	P	655	ENSP00000331678:R655P	ENSP00000331678:R655P	R	+	2	0	PKP3	393658	1.000000	0.71417	0.995000	0.50966	0.471000	0.32888	7.439000	0.80444	2.172000	0.68678	0.306000	0.20318	CGT	G|0.999;C|0.001	0.001	strong		0.667	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
AVIL	10677	hgsc.bcm.edu	37	12	58204648	58204648	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58204648A>G	ENST00000257861.3	-	5	939	c.509T>C	c.(508-510)gTc>gCc	p.V170A	AVIL_ENST00000537081.1_Missense_Mutation_p.V163A	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	170	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TTGGATGATGACTTTCCCAAG	0.488																																					p.V170A		Atlas-SNP	.											.	AVIL	60	.	0			c.T509C						PASS	.						152.0	150.0	151.0					12																	58204648		2203	4300	6503	SO:0001583	missense	10677	exon5			ATGATGACTTTCC	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.509T>C	12.37:g.58204648A>G	ENSP00000257861:p.Val170Ala	91.0	0.0	0		132.0	6.0	0.0454545	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	A	8.559	0.877295	0.17395	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.52983	0.64;0.64	5.35	3.02	0.34903	Gelsolin domain (1);	0.304736	0.36066	N	0.002805	T	0.29684	0.0741	L	0.34521	1.04	0.28434	N	0.917138	B;B	0.02656	0.0;0.0	B;B	0.12156	0.007;0.005	T	0.24404	-1.0161	10	0.08381	T	0.77	-20.9205	7.3653	0.26770	0.7523:0.0:0.2477:0.0	.	163;170	O75366-2;O75366	.;AVIL_HUMAN	A	163;170	ENSP00000443207:V163A;ENSP00000257861:V170A	ENSP00000257861:V170A	V	-	2	0	AVIL	56490915	0.024000	0.19004	1.000000	0.80357	0.953000	0.61014	0.322000	0.19576	0.490000	0.27771	0.533000	0.62120	GTC	.	.	none		0.488	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576	
POLQ	10721	hgsc.bcm.edu	37	3	121251922	121251922	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121251922A>G	ENST00000264233.5	-	6	1003	c.875T>C	c.(874-876)cTt>cCt	p.L292P	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	292					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TGACTCCAAAAGCGGTACAGG	0.428								DNA polymerases (catalytic subunits)																													p.L292P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T875C						PASS	.						93.0	92.0	92.0					3																	121251922		2203	4300	6503	SO:0001583	missense	10721	exon6			TCCAAAAGCGGTA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.875T>C	3.37:g.121251922A>G	ENSP00000264233:p.Leu292Pro	228.0	0.0	0		237.0	66.0	0.278481	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.089579	0.76756	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.67698	-0.28	5.29	5.29	0.74685	DEAD-like helicase (1);	0.063724	0.64402	D	0.000005	D	0.87026	0.6075	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91012	0.4850	10	0.87932	D	0	.	15.5172	0.75833	1.0:0.0:0.0:0.0	.	292	O75417	DPOLQ_HUMAN	P	292;427	ENSP00000264233:L292P	ENSP00000264233:L292P	L	-	2	0	POLQ	122734612	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	8.851000	0.92205	2.126000	0.65437	0.377000	0.23210	CTT	.	.	none		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MYH9	4627	hgsc.bcm.edu	37	22	36690158	36690158	+	Missense_Mutation	SNP	C	C	T	rs147031322		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36690158C>T	ENST00000216181.5	-	28	4047	c.3817G>A	c.(3817-3819)Gac>Aac	p.D1273N		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1273					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.D1273N(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GTGACCTTGTCGGCCAGCTCT	0.657			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.D1273N		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	MYH9,rectum,carcinoma,0,1	MYH9	225	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3817A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	68.0	65.0	66.0		3817	5.0	1.0	22	dbSNP_134	66	2,8598	2.2+/-6.3	0,2,4298	no	missense	MYH9	NM_002473.4	23	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1273/1961	36690158	2,13004	2203	4300	6503	SO:0001583	missense	4627	exon28	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTTGTCGGCCAG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.3817G>A	22.37:g.36690158C>T	ENSP00000216181:p.Asp1273Asn	48.0	0.0	0		49.0	20.0	0.408163	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.608292	0.87258	0.0	2.33E-4	ENSG00000100345	ENST00000216181	D	0.82893	-1.66	4.98	4.98	0.66077	Myosin tail (1);	0.107359	0.64402	D	0.000006	T	0.77096	0.4080	N	0.20986	0.625	0.80722	D	1	B	0.28178	0.202	B	0.35353	0.201	T	0.72497	-0.4275	10	0.25751	T	0.34	.	18.6261	0.91340	0.0:1.0:0.0:0.0	.	1273	P35579	MYH9_HUMAN	N	1273	ENSP00000216181:D1273N	ENSP00000216181:D1273N	D	-	1	0	MYH9	35020104	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.954000	0.70298	2.454000	0.82982	0.561000	0.74099	GAC	C|1.000;T|0.000	0.000	weak		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
ZNF285	26974	hgsc.bcm.edu	37	19	44890654	44890654	+	Missense_Mutation	SNP	C	C	T	rs149238831	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44890654C>T	ENST00000330997.4	-	4	1817	c.1753G>A	c.(1753-1755)Gag>Aag	p.E585K	ZNF285_ENST00000544719.2_Missense_Mutation_p.E585K|ZNF285_ENST00000591679.1_Missense_Mutation_p.E592K|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	585					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TCTCTCTGCTCATGTAGTCTT	0.418																																					p.E585K		Atlas-SNP	.											.	ZNF285	86	.	0			c.G1753A						PASS	.						127.0	107.0	113.0					19																	44890654		2203	4300	6503	SO:0001583	missense	26974	exon4			TCTGCTCATGTAG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1753G>A	19.37:g.44890654C>T	ENSP00000333595:p.Glu585Lys	108.0	0.0	0		100.0	15.0	0.15	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	3.493	-0.103371	0.06967	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.05996	3.36	1.94	-3.87	0.04218	.	.	.	.	.	T	0.02494	0.0076	N	0.26092	0.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41124	-0.9526	9	0.87932	D	0	.	1.2743	0.02027	0.168:0.3012:0.3374:0.1934	.	609;585	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	K	608;585	ENSP00000333595:E585K	ENSP00000333595:E585K	E	-	1	0	ZNF285	49582494	0.793000	0.28825	0.000000	0.03702	0.035000	0.12851	0.746000	0.26275	-1.954000	0.01025	0.454000	0.30748	GAG	C|0.995;T|0.005	0.005	strong		0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
IVL	3713	hgsc.bcm.edu	37	1	152882648	152882648	+	Missense_Mutation	SNP	A	A	C	rs572279454	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152882648A>C	ENST00000368764.3	+	2	439	c.375A>C	c.(373-375)gaA>gaC	p.E125D	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	125					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCTGGAAGAAGAGAAGAAGC	0.473																																					p.E125D		Atlas-SNP	.											.	IVL	100	.	0			c.A375C						PASS	.						61.0	66.0	64.0					1																	152882648		2203	4300	6503	SO:0001583	missense	3713	exon2			GGAAGAAGAGAAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.375A>C	1.37:g.152882648A>C	ENSP00000357753:p.Glu125Asp	82.0	0.0	0		79.0	11.0	0.139241	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.461146	0.43736	.	.	ENSG00000163207	ENST00000368764	T	0.09073	3.02	4.61	-0.221	0.13126	.	.	.	.	.	T	0.02119	0.0066	L	0.40543	1.245	0.30851	N	0.734551	P	0.47409	0.895	B	0.41236	0.351	T	0.47381	-0.9122	9	0.36615	T	0.2	0.146	3.861	0.08996	0.4357:0.0:0.4003:0.164	.	125	P07476	INVO_HUMAN	D	125	ENSP00000357753:E125D	ENSP00000357753:E125D	E	+	3	2	IVL	151149272	0.000000	0.05858	0.010000	0.14722	0.344000	0.29017	0.286000	0.18902	0.134000	0.18681	0.358000	0.22013	GAA	.	.	none		0.473	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
FNDC8	54752	hgsc.bcm.edu	37	17	33454198	33454198	+	Missense_Mutation	SNP	G	G	T	rs147725468		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33454198G>T	ENST00000158009.5	+	2	462	c.347G>T	c.(346-348)gGg>gTg	p.G116V		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	116						nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		ATGCTGGAGGGGGAGCTGAAC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		20327	0.0		0.001	False		,,,				2504	0.0				p.G116V		Atlas-SNP	.											.	FNDC8	28	.	0			c.G347T						PASS	.	G	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	133.0	136.0	135.0		347	5.4	0.2	17	dbSNP_134	135	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FNDC8	NM_017559.2	109	0,12,6491	TT,TG,GG		0.1163,0.0454,0.0923	probably-damaging	116/325	33454198	12,12994	2203	4300	6503	SO:0001583	missense	54752	exon2			TGGAGGGGGAGCT	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"""Fibronectin type III domain containing"""	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.347G>T	17.37:g.33454198G>T	ENSP00000158009:p.Gly116Val	61.0	0.0	0		84.0	49.0	0.583333	NM_017559	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	37	CCDS11290.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.4	3.975927	0.74360	4.54E-4	0.001163	ENSG00000073598	ENST00000158009	T	0.35973	1.28	5.38	5.38	0.77491	.	0.000000	0.50627	D	0.000111	T	0.46776	0.1410	L	0.27053	0.805	0.46521	D	0.999088	D	0.89917	1.0	D	0.74674	0.984	T	0.45086	-0.9285	10	0.87932	D	0	-20.0231	14.5032	0.67737	0.0:0.0:1.0:0.0	.	116	Q8TC99	FNDC8_HUMAN	V	116	ENSP00000158009:G116V	ENSP00000158009:G116V	G	+	2	0	FNDC8	30478311	0.998000	0.40836	0.228000	0.23943	0.985000	0.73830	4.167000	0.58209	2.794000	0.96219	0.655000	0.94253	GGG	G|0.999;T|0.001	0.001	strong		0.567	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559	
IL10RA	3587	hgsc.bcm.edu	37	11	117869878	117869878	+	Missense_Mutation	SNP	C	C	T	rs2229114	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117869878C>T	ENST00000227752.3	+	7	1379	c.1259C>T	c.(1258-1260)tCg>tTg	p.S420L	IL10RA_ENST00000541785.1_Missense_Mutation_p.S400L|IL10RA_ENST00000545409.1_Missense_Mutation_p.S271L|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	420			S -> L (in dbSNP:rs2229114). {ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CAGGGTGGCTCGGCCTTGGGC	0.622													C|||	84	0.0167732	0.0015	0.0533	5008	,	,		18104	0.0		0.0427	False		,,,				2504	0.002				p.S420L		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1259T						PASS	.	C	LEU/SER	49,4351	50.2+/-85.5	0,49,2151	47.0	50.0	49.0		1259	1.8	0.0	11	dbSNP_98	49	422,8170	131.5+/-189.3	13,396,3887	yes	missense	IL10RA	NM_001558.3	145	13,445,6038	TT,TC,CC		4.9115,1.1136,3.6253	probably-damaging	420/579	117869878	471,12521	2200	4296	6496	SO:0001583	missense	3587	exon7			GTGGCTCGGCCTT	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1259C>T	11.37:g.117869878C>T	ENSP00000227752:p.Ser420Leu	96.0	0.0	0		116.0	107.0	0.922414	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	62	0.028388278388278388	3	0.006097560975609756	22	0.06077348066298342	0	0.0	37	0.048812664907651716	C	14.11	2.437539	0.43224	0.011136	0.049115	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.33654	1.4;1.4;1.4	5.93	1.82	0.25136	.	1.134890	0.06593	N	0.752483	T	0.03783	0.0107	M	0.67953	2.075	0.09310	N	1	P;B	0.37233	0.588;0.317	B;B	0.29524	0.103;0.026	T	0.21348	-1.0248	10	0.66056	D	0.02	-7.4946	2.3827	0.04358	0.1435:0.4211:0.2787:0.1567	rs2229114;rs2229114	400;420	F5GYV8;Q13651	.;I10R1_HUMAN	L	420;400;271;400	ENSP00000227752:S420L;ENSP00000441397:S400L;ENSP00000443019:S271L	ENSP00000227752:S420L	S	+	2	0	IL10RA	117375088	0.001000	0.12720	0.025000	0.17156	0.054000	0.15201	0.608000	0.24223	0.420000	0.25954	0.563000	0.77884	TCG	C|0.969;T|0.031	0.031	strong		0.622	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
SPTLC3	55304	hgsc.bcm.edu	37	20	13145471	13145471	+	Missense_Mutation	SNP	G	G	A	rs200308499		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13145471G>A	ENST00000399002.2	+	12	1890	c.1616G>A	c.(1615-1617)cGt>cAt	p.R539H		NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	539					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						AAGTCAGCACGTCCTGAGCTC	0.443																																					p.R539H		Atlas-SNP	.											.	SPTLC3	78	.	0			c.G1616A						PASS	.	G	HIS/ARG	1,3895		0,1,1947	91.0	85.0	87.0		1616	-1.5	0.0	20		87	0,8278		0,0,4139	yes	missense	SPTLC3	NM_018327.2	29	0,1,6086	AA,AG,GG		0.0,0.0257,0.0082	benign	539/553	13145471	1,12173	1948	4139	6087	SO:0001583	missense	55304	exon12			CAGCACGTCCTGA	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.1616G>A	20.37:g.13145471G>A	ENSP00000381968:p.Arg539His	89.0	0.0	0		94.0	28.0	0.297872	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	G	7.900	0.734107	0.15574	2.57E-4	0.0	ENSG00000172296	ENST00000399002	D	0.95885	-3.84	5.69	-1.45	0.08828	.	0.883465	0.09800	U	0.754214	D	0.89622	0.6768	N	0.16743	0.435	0.19300	N	0.999975	B	0.11235	0.004	B	0.06405	0.002	T	0.77547	-0.2547	10	0.41790	T	0.15	-1.3251	12.8449	0.57823	0.4423:0.0:0.5577:0.0	.	539	Q9NUV7	SPTC3_HUMAN	H	539	ENSP00000381968:R539H	ENSP00000381968:R539H	R	+	2	0	SPTLC3	13093471	0.035000	0.19736	0.002000	0.10522	0.074000	0.17049	0.997000	0.29731	-0.126000	0.11682	-0.136000	0.14681	CGT	.	.	weak		0.443	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
RICTOR	253260	hgsc.bcm.edu	37	5	38944635	38944635	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:38944635C>T	ENST00000357387.3	-	36	4856	c.4826G>A	c.(4825-4827)cGt>cAt	p.R1609H	RICTOR_ENST00000296782.5_Missense_Mutation_p.R1633H	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AAGGAGTATACGGCACATTGG	0.323																																					p.R1609H		Atlas-SNP	.											RICTOR,colon,carcinoma,0,1	RICTOR	182	1	0			c.G4826A						PASS	.						101.0	98.0	99.0					5																	38944635		2203	4300	6503	SO:0001583	missense	253260	exon36			AGTATACGGCACA		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.4826G>A	5.37:g.38944635C>T	ENSP00000349959:p.Arg1609His	60.0	0.0	0		73.0	4.0	0.0547945	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.397706	0.96009	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.53857	0.62;0.6	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	L	0.56769	1.78	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.57152	0.747;0.814	T	0.69262	-0.5191	10	0.87932	D	0	-14.5494	19.4767	0.94992	0.0:1.0:0.0:0.0	.	1609;1633	Q6R327;Q6R327-3	RICTR_HUMAN;.	H	1609;1633	ENSP00000349959:R1609H;ENSP00000296782:R1633H	ENSP00000296782:R1633H	R	-	2	0	RICTOR	38980392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.366000	0.59492	2.601000	0.87937	0.563000	0.77884	CGT	.	.	none		0.323	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
B3GNT5	84002	hgsc.bcm.edu	37	3	182988131	182988131	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182988131A>G	ENST00000326505.3	+	2	1075	c.545A>G	c.(544-546)tAt>tGt	p.Y182C	MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.Y182C|B3GNT5_ENST00000460419.1_Missense_Mutation_p.Y182C|MCF2L2_ENST00000473233.1_Intron	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	182					cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycolipid biosynthetic process (GO:0009247)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity (GO:0008457)|galactosyltransferase activity (GO:0008378)|lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity (GO:0047256)|lipopolysaccharide N-acetylglucosaminyltransferase activity (GO:0008917)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			GCAAATACCTATTGTCCACAT	0.333																																					p.Y182C		Atlas-SNP	.											.	B3GNT5	26	.	0			c.A545G						PASS	.						94.0	93.0	94.0					3																	182988131		2203	4300	6503	SO:0001583	missense	84002	exon2			ATACCTATTGTCC	AB045278	CCDS3244.1	3q28	2013-02-21			ENSG00000176597	ENSG00000176597	2.4.1.206	"""Beta 3-glycosyltransferases"""	15684	protein-coding gene	gene with protein product	"""lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase"""	615333				11283017	Standard	XM_005247824		Approved	B3GN-T5, beta3Gn-T5	uc003flk.3	Q9BYG0	OTTHUMG00000158436	ENST00000326505.3:c.545A>G	3.37:g.182988131A>G	ENSP00000316173:p.Tyr182Cys	168.0	0.0	0		156.0	69.0	0.442308	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	37	CCDS3244.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598341	0.46318	.	.	ENSG00000176597	ENST00000326505;ENST00000460419;ENST00000465010	T;T;T	0.44083	0.93;0.93;0.93	5.91	1.73	0.24493	.	0.273852	0.36665	N	0.002479	T	0.59715	0.2214	M	0.89658	3.05	0.39485	D	0.96795	D	0.56968	0.978	P	0.53722	0.733	T	0.68364	-0.5428	10	0.56958	D	0.05	.	11.4792	0.50316	0.578:0.0:0.0:0.422	.	182	Q9BYG0	B3GN5_HUMAN	C	182	ENSP00000316173:Y182C;ENSP00000420778:Y182C;ENSP00000417868:Y182C	ENSP00000316173:Y182C	Y	+	2	0	B3GNT5	184470825	1.000000	0.71417	0.858000	0.33744	0.985000	0.73830	2.639000	0.46570	0.399000	0.25367	-0.451000	0.05528	TAT	.	.	none		0.333	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047	
ERBB4	2066	hgsc.bcm.edu	37	2	212251864	212251864	+	Silent	SNP	T	T	C	rs3748962	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:212251864T>C	ENST00000342788.4	-	27	3505	c.3195A>G	c.(3193-3195)gtA>gtG	p.V1065V	ERBB4_ENST00000402597.1_Silent_p.V1055V|ERBB4_ENST00000436443.1_Silent_p.V1049V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1065					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CATCTCGGTATACAAACTGGT	0.433										TSP Lung(8;0.080)			T|||	1117	0.223043	0.0756	0.2983	5008	,	,		18765	0.2887		0.2992	False		,,,				2504	0.2229				p.V1065V		Atlas-SNP	.											.	ERBB4	480	.	0			c.A3195G						PASS	.	T	,	444,3962	214.5+/-233.7	29,386,1788	110.0	113.0	112.0		3147,3195	-8.9	0.3	2	dbSNP_107	112	2843,5757	447.9+/-361.7	499,1845,1956	no	coding-synonymous,coding-synonymous	ERBB4	NM_001042599.1,NM_005235.2	,	528,2231,3744	CC,CT,TT		33.0581,10.0772,25.273	,	1049/1293,1065/1309	212251864	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	2066	exon27			TCGGTATACAAAC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3195A>G	2.37:g.212251864T>C		165.0	0.0	0		189.0	92.0	0.486772	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																			T|0.756;C|0.244	0.244	strong		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
FHOD1	29109	hgsc.bcm.edu	37	16	67281172	67281172	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:67281172C>T	ENST00000258201.4	-	1	389	c.142G>A	c.(142-144)Gcg>Acg	p.A48T	SLC9A5_ENST00000299798.11_5'Flank	NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	48					positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		AAGGGCAGCGCCCCGTCCAGG	0.697																																					p.A48T		Atlas-SNP	.											.	FHOD1	86	.	0			c.G142A						PASS	.						20.0	21.0	21.0					16																	67281172		2192	4296	6488	SO:0001583	missense	29109	exon1			GCAGCGCCCCGTC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.142G>A	16.37:g.67281172C>T	ENSP00000258201:p.Ala48Thr	16.0	0.0	0		11.0	6.0	0.545455	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.488654	0.64074	.	.	ENSG00000135723	ENST00000258201	T	0.23754	1.89	5.39	5.39	0.77823	.	0.191112	0.38959	N	0.001503	T	0.17195	0.0413	L	0.27053	0.805	0.80722	D	1	B	0.19706	0.038	B	0.10450	0.005	T	0.08146	-1.0736	10	0.19147	T	0.46	.	11.5832	0.50904	0.0:0.9188:0.0:0.0812	.	48	Q9Y613	FHOD1_HUMAN	T	48	ENSP00000258201:A48T	ENSP00000258201:A48T	A	-	1	0	FHOD1	65838673	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.705000	0.37867	2.536000	0.85505	0.561000	0.74099	GCG	.	.	none		0.697	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
SGK1	6446	hgsc.bcm.edu	37	6	134495200	134495200	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495200G>C	ENST00000237305.7	-	3	259	c.171C>G	c.(169-171)atC>atG	p.I57M	SGK1_ENST00000528577.1_Missense_Mutation_p.I85M|SGK1_ENST00000413996.3_Missense_Mutation_p.I71M|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.I47M|SGK1_ENST00000475719.2_Missense_Mutation_p.I57M|SGK1_ENST00000367858.5_Missense_Mutation_p.I152M	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	57	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGATCTTCAAGATGGACTGAA	0.493																																					p.I152M		Atlas-SNP	.											.	SGK1	387	.	0			c.C456G						PASS	.						133.0	125.0	128.0					6																	134495200		2203	4300	6503	SO:0001583	missense	6446	exon5			CTTCAAGATGGAC	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.171C>G	6.37:g.134495200G>C	ENSP00000237305:p.Ile57Met	72.0	0.0	0		76.0	5.0	0.0657895	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056994	0.36277	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38887	1.58;1.58;1.58;1.58;1.58;1.58;1.11	5.99	4.87	0.63330	.	0.090924	0.85682	D	0.000000	T	0.12944	0.0314	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.27192	0.171;0.053;0.004;0.021;0.006;0.022	B;B;B;B;B;B	0.25291	0.059;0.013;0.005;0.041;0.016;0.018	T	0.06075	-1.0847	10	0.41790	T	0.15	.	6.963	0.24608	0.7211:0.0:0.2789:0.0	.	85;71;57;47;152;57	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	M	152;71;57;47;85;57;121	ENSP00000356832:I152M;ENSP00000396242:I71M;ENSP00000237305:I57M;ENSP00000356831:I47M;ENSP00000434450:I85M;ENSP00000434302:I57M;ENSP00000435577:I121M	ENSP00000237305:I57M	I	-	3	3	SGK1	134536893	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.721000	0.38032	1.147000	0.42369	0.655000	0.94253	ATC	.	.	none		0.493	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
SNAP25	6616	hgsc.bcm.edu	37	20	10258375	10258375	+	Splice_Site	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10258375G>A	ENST00000254976.2	+	3	325		c.e3+1		SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000304886.2_Splice_Site	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa						energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	GGTTGAAGAGGTAAGAAGTGA	0.398																																					.		Atlas-SNP	.											.	SNAP25	79	.	0			c.114+1G>A						PASS	.						103.0	92.0	95.0					20																	10258375		2203	4300	6503	SO:0001630	splice_region_variant	6616	exon3			GAAGAGGTAAGAA		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"""resistance to inhibitors of cholinesterase 4 homolog"""	600322	"""synaptosomal-associated protein, 25kD"""	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.114+1G>A	20.37:g.10258375G>A		40.0	0.0	0		20.0	5.0	0.25	NM_130811	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Splice_Site	SNP	ENST00000254976.2	37	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911425	0.72983	.	.	ENSG00000132639	ENST00000254976;ENST00000304886;ENST00000430336	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5584	0.95363	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNAP25	10206375	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.749000	0.91619	2.618000	0.88619	0.655000	0.94253	.	.	.	none		0.398	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811	Intron
MRPL45	84311	hgsc.bcm.edu	37	17	36453167	36453167	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:36453167T>C	ENST00000312513.5	+	1	179	c.18T>C	c.(16-18)ccT>ccC	p.P6P		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	6						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CCCCCATACCTCAAGGGTTCT	0.597																																					p.P6P		Atlas-SNP	.											.	MRPL45	27	.	0			c.T18C						PASS	.						105.0	103.0	104.0					17																	36453167		692	1591	2283	SO:0001819	synonymous_variant	84311	exon1			CATACCTCAAGGG	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.18T>C	17.37:g.36453167T>C		51.0	0.0	0		67.0	20.0	0.298507	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	37	CCDS11326.1																																																																																			.	.	none		0.597	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
STAT3	6774	hgsc.bcm.edu	37	17	40475330	40475330	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40475330C>A	ENST00000264657.5	-	19	2008	c.1696G>T	c.(1696-1698)Gac>Tac	p.D566Y	STAT3_ENST00000404395.3_Missense_Mutation_p.D566Y|STAT3_ENST00000585517.1_Missense_Mutation_p.D566Y|STAT3_ENST00000389272.3_Missense_Mutation_p.D468Y|STAT3_ENST00000588969.1_Missense_Mutation_p.D566Y	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	566					acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D566N(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		ATGATATTGTCCAGCCAGACC	0.507									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D566Y		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,1	STAT3	268	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1696T						PASS	.						111.0	105.0	107.0					17																	40475330		2203	4300	6503	SO:0001583	missense	6774	exon19	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TATTGTCCAGCCA	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1696G>T	17.37:g.40475330C>A	ENSP00000264657:p.Asp566Tyr	87.0	0.0	0	893	102.0	33.0	0.323529	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120901	0.94385	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89343	-2.5;-2.5;-2.5	5.9	5.9	0.94986	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.89347	0.6689	L	0.31157	0.91	0.80722	D	1	P;P;P	0.41131	0.693;0.739;0.739	P;P;P	0.51266	0.533;0.664;0.664	D	0.87296	0.2302	10	0.35671	T	0.21	-26.7334	20.2754	0.98485	0.0:1.0:0.0:0.0	.	566;566;566	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	Y	566;468;566	ENSP00000264657:D566Y;ENSP00000373923:D468Y;ENSP00000384943:D566Y	ENSP00000264657:D566Y	D	-	1	0	STAT3	37728856	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.708000	0.84633	2.793000	0.96121	0.609000	0.83330	GAC	.	.	none		0.507	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552201	102552201	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102552201A>G	ENST00000216281.8	-	3	628	c.423T>C	c.(421-423)gcT>gcC	p.A141A	HSP90AA1_ENST00000334701.7_Silent_p.A263A|HSP90AA1_ENST00000441629.2_Intron	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	141					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	CAACCAAATAAGCAGAATAAA	0.473																																					p.A263A		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.T789C						PASS	.						86.0	82.0	84.0					14																	102552201		2203	4300	6503	SO:0001819	synonymous_variant	3320	exon4			CAAATAAGCAGAA	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.423T>C	14.37:g.102552201A>G		136.0	0.0	0		155.0	40.0	0.258065	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	37	CCDS9967.1																																																																																			.	.	none		0.473	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
PTPRD	5789	hgsc.bcm.edu	37	9	8449782	8449782	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:8449782G>A	ENST00000381196.4	-	31	4474	c.3931C>T	c.(3931-3933)Cct>Tct	p.P1311S	PTPRD_ENST00000540109.1_Missense_Mutation_p.P1311S|PTPRD_ENST00000356435.5_Missense_Mutation_p.P1311S|PTPRD_ENST00000486161.1_Missense_Mutation_p.P904S|PTPRD_ENST00000358503.5_Missense_Mutation_p.P1289S|PTPRD_ENST00000355233.5_Missense_Mutation_p.P905S|PTPRD_ENST00000397606.3_Missense_Mutation_p.P890S|PTPRD_ENST00000360074.4_Missense_Mutation_p.P1298S|PTPRD_ENST00000397617.3_Missense_Mutation_p.P890S|PTPRD_ENST00000397611.3_Missense_Mutation_p.P901S|PTPRD_ENST00000537002.1_Missense_Mutation_p.P901S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1311					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TGGTGTGAAGGGATCTCCTTA	0.433										TSP Lung(15;0.13)																											p.P1311S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.C3931T						PASS	.						373.0	343.0	353.0					9																	8449782		2203	4300	6503	SO:0001583	missense	5789	exon34			GTGAAGGGATCTC	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3931C>T	9.37:g.8449782G>A	ENSP00000370593:p.Pro1311Ser	228.0	0.0	0		189.0	57.0	0.301587	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167160	0.38217	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.52295	0.71;0.71;0.74;0.79;0.89;0.99;0.79;0.67;0.71;0.9;0.99	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.28599	0.0708	N	0.04203	-0.255	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.33612	0.295;0.295;0.295;0.295;0.003;0.419;0.002;0.001;0.001	B;B;B;B;B;B;B;B;B	0.32342	0.068;0.068;0.068;0.068;0.01;0.144;0.007;0.002;0.002	T	0.12477	-1.0546	9	.	.	.	.	19.9455	0.97180	0.0:0.0:1.0:0.0	.	890;895;904;905;901;901;1298;1311;1311	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	1311;1311;1298;1289;905;890;901;901;782;1311;904;890	ENSP00000370593:P1311S;ENSP00000348812:P1311S;ENSP00000353187:P1298S;ENSP00000351293:P1289S;ENSP00000347373:P905S;ENSP00000380741:P890S;ENSP00000380735:P901S;ENSP00000440515:P901S;ENSP00000438164:P1311S;ENSP00000417093:P904S;ENSP00000380731:P890S	.	P	-	1	0	PTPRD	8439782	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.143000	0.71756	2.788000	0.95919	0.650000	0.86243	CCT	.	.	none		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
TAS1R2	80834	hgsc.bcm.edu	37	1	19175944	19175944	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19175944C>T	ENST00000375371.3	-	4	1379	c.1358G>A	c.(1357-1359)tGg>tAg	p.W453*	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	453					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GTCCCATTGCCACTGGACAAT	0.567																																					p.W453X		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G1358A						PASS	.						101.0	88.0	92.0					1																	19175944		2203	4300	6503	SO:0001587	stop_gained	80834	exon4			CATTGCCACTGGA		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1358G>A	1.37:g.19175944C>T	ENSP00000364520:p.Trp453*	86.0	0.0	0		92.0	4.0	0.0434783	NM_152232	Q5TZ19	Nonsense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.228655	0.58777	.	.	ENSG00000179002	ENST00000375371	.	.	.	4.49	3.57	0.40892	.	0.561733	0.15487	N	0.259793	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.754	0.40492	0.2057:0.7943:0.0:0.0	.	.	.	.	X	453	.	ENSP00000364520:W453X	W	-	2	0	TAS1R2	19048531	1.000000	0.71417	1.000000	0.80357	0.231000	0.25187	5.144000	0.64832	1.091000	0.41335	0.561000	0.74099	TGG	.	.	none		0.567	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
OR2W5	441932	hgsc.bcm.edu	37	1	247655102	247655102	+	RNA	SNP	G	G	A	rs143904230	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247655102G>A	ENST00000522351.1	+	0	733							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TTGCAGCCGCGGTGCTGAGGA	0.567													G|||	29	0.00579073	0.0023	0.0144	5008	,	,		18573	0.0		0.0129	False		,,,				2504	0.0031				p.G225S		Atlas-SNP	.											.	OR2W5	97	.	0			c.G673A						PASS	.	G	SER/GLY	11,4395	17.9+/-39.9	0,11,2192	120.0	114.0	116.0		673	-4.1	0.1	1	dbSNP_134	116	137,8463	69.7+/-132.2	1,135,4164	yes	missense	OR2W5	NM_001004698.2	56	1,146,6356	AA,AG,GG		1.593,0.2497,1.1379	benign	225/321	247655102	148,12858	2203	4300	6503			441932	exon1			AGCCGCGGTGCTG			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247655102G>A		76.0	0.0	0		94.0	60.0	0.638298	NM_001004698	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																				G|0.989;A|0.011	0.011	strong		0.567	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
NOS1	4842	hgsc.bcm.edu	37	12	117672544	117672544	+	Missense_Mutation	SNP	G	G	A	rs375069851		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:117672544G>A	ENST00000338101.4	-	21	3167	c.3163C>T	c.(3163-3165)Cgt>Tgt	p.R1055C	NOS1_ENST00000317775.6_Missense_Mutation_p.R1021C|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTGTGGAGACGCACGAAGATA	0.552																																					p.R1055C	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,caecum,carcinoma,0,2	NOS1	240	2	0			c.C3163T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4080		0,0,2040	35.0	39.0	38.0		3061,2053,2053,3163	4.7	1.0	12		38	2,8402		0,2,4200	no	missense,missense,missense,missense	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	180,180,180,180	0,2,6240	AA,AG,GG		0.0238,0.0,0.016	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1021/1435,685/1099,685/1099,1055/1469	117672544	2,12482	2040	4202	6242	SO:0001583	missense	4842	exon22			GGAGACGCACGAA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3163C>T	12.37:g.117672544G>A	ENSP00000337459:p.Arg1055Cys	72.0	0.0	0		68.0	26.0	0.382353	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603856	0.46423	0.0	2.38E-4	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.67698	-0.28;-0.28	4.65	4.65	0.58169	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.056224	0.85682	D	0.000000	T	0.79227	0.4410	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.81560	-0.0877	10	0.87932	D	0	-17.9866	18.067	0.89394	0.0:0.0:1.0:0.0	.	1021	P29475	NOS1_HUMAN	C	916;1021;1021;1055	ENSP00000320758:R1021C;ENSP00000337459:R1055C	ENSP00000320758:R1021C	R	-	1	0	NOS1	116156927	1.000000	0.71417	1.000000	0.80357	0.210000	0.24377	4.455000	0.60075	2.568000	0.86640	0.561000	0.74099	CGT	.	.	weak		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
BST1	683	hgsc.bcm.edu	37	4	15720553	15720553	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:15720553T>C	ENST00000265016.4	+	7	923	c.728T>C	c.(727-729)aTg>aCg	p.M243T	BST1_ENST00000382346.3_Missense_Mutation_p.M258T	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	243					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						GAAGGCAGCATGAAAGTCCTG	0.403																																					p.M243T		Atlas-SNP	.											.	BST1	30	.	0			c.T728C						PASS	.						113.0	108.0	110.0					4																	15720553		2203	4300	6503	SO:0001583	missense	683	exon7			GCAGCATGAAAGT	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.728T>C	4.37:g.15720553T>C	ENSP00000265016:p.Met243Thr	82.0	0.0	0		79.0	38.0	0.481013	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.727|8.727	0.915766|0.915766	0.17907|0.17907	.|.	.|.	ENSG00000109743|ENSG00000109743	ENST00000265016;ENST00000382346;ENST00000514445|ENST00000505785;ENST00000514989	T;T;T|.	0.17213|.	2.29;2.29;2.29|.	4.75|4.75	4.75|4.75	0.60458|0.60458	NAD(P)-binding domain (1);|.	0.412136|.	0.23912|.	N|.	0.043325|.	T|.	0.38983|.	0.1061|.	L|L	0.36672|0.36672	1.1|1.1	0.26095|0.26095	N|N	0.980894|0.980894	B;B|.	0.31125|.	0.309;0.309|.	B;B|.	0.33568|.	0.166;0.166|.	T|.	0.24119|.	-1.0169|.	10|.	0.72032|.	D|.	0.01|.	-15.8415|-15.8415	10.8134|10.8134	0.46559|0.46559	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	258;243|.	A6NC48;Q10588|.	.;BST1_HUMAN|.	T|R	243;258;93|139;51	ENSP00000265016:M243T;ENSP00000371783:M258T;ENSP00000420925:M93T|.	ENSP00000265016:M243T|.	M|X	+|+	2|1	0|0	BST1|BST1	15329651|15329651	1.000000|1.000000	0.71417|0.71417	0.946000|0.946000	0.38457|0.38457	0.127000|0.127000	0.20565|0.20565	4.043000|4.043000	0.57354|0.57354	2.128000|2.128000	0.65567|0.65567	0.528000|0.528000	0.53228|0.53228	ATG|TGA	.	.	none		0.403	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
PAIP2B	400961	hgsc.bcm.edu	37	2	71415619	71415619	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71415619T>C	ENST00000244221.8	-	4	528	c.362A>G	c.(361-363)gAg>gGg	p.E121G		NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	121					negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)			large_intestine(1)|lung(1)	2						TCAGTACTTCTCTCCTGGAAT	0.458																																					p.E121G		Atlas-SNP	.											.	PAIP2B	7	.	0			c.A362G						PASS	.						90.0	84.0	86.0					2																	71415619		1870	4114	5984	SO:0001583	missense	400961	exon4			TACTTCTCTCCTG		CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374			29200	protein-coding gene	gene with protein product		611018				16804161	Standard	NM_020459		Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.362A>G	2.37:g.71415619T>C	ENSP00000244221:p.Glu121Gly	143.0	0.0	0		80.0	54.0	0.675	NM_020459		Missense_Mutation	SNP	ENST00000244221.8	37	CCDS46322.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.545159	0.45280	.	.	ENSG00000124374	ENST00000244221	.	.	.	5.4	4.23	0.50019	.	0.224838	0.38381	N	0.001705	T	0.34978	0.0916	N	0.14661	0.345	0.33638	D	0.606887	B	0.10296	0.003	B	0.12837	0.008	T	0.41324	-0.9515	9	0.72032	D	0.01	-12.7367	9.9702	0.41749	0.8459:0.0:0.0:0.1541	.	121	Q9ULR5	PAI2B_HUMAN	G	121	.	ENSP00000244221:E121G	E	-	2	0	PAIP2B	71269127	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.295000	0.65692	0.869000	0.35703	-0.917000	0.02746	GAG	.	.	none		0.458	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330547.2	XM_376062	
OR4K17	390436	hgsc.bcm.edu	37	14	20585769	20585769	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20585769C>T	ENST00000315543.4	+	1	204	c.204C>T	c.(202-204)gtC>gtT	p.V68V		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TCTATGTGGTCACAGTTTTGG	0.398																																					p.V68V		Atlas-SNP	.											.	OR4K17	58	.	0			c.C204T						PASS	.						305.0	290.0	295.0					14																	20585769		2203	4300	6503	SO:0001819	synonymous_variant	390436	exon1			TGTGGTCACAGTT		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.204C>T	14.37:g.20585769C>T		267.0	0.0	0		205.0	95.0	0.463415	NM_001004715	Q6IF12	Silent	SNP	ENST00000315543.4	37	CCDS32030.1																																																																																			.	.	none		0.398	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
MRGPRG	386746	hgsc.bcm.edu	37	11	3239366	3239366	+	Silent	SNP	G	G	A	rs145777944	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3239366G>A	ENST00000332314.3	-	1	677	c.678C>T	c.(676-678)ttC>ttT	p.F226F	MRGPRG-AS1_ENST00000420873.2_RNA|MRGPRG-AS1_ENST00000434798.1_RNA	NM_001164377.1	NP_001157849.1	Q86SM5	MRGRG_HUMAN	MAS-related GPR, member G	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)										CGGGCAGCAGGAAGTTCAGCA	0.667													G|||	8	0.00159744	0.0023	0.0	5008	,	,		13867	0.0		0.002	False		,,,				2504	0.0031				p.F226F		Atlas-SNP	.											.	MRGPRG	6	.	0			c.C678T						PASS	.						46.0	57.0	53.0					11																	3239366		692	1588	2280	SO:0001819	synonymous_variant	386746	exon1			CAGCAGGAAGTTC	AY255583	CCDS44520.1	11p15.4	2012-08-21	2004-03-25		ENSG00000182170	ENSG00000182170		"""GPCR / Class A : Orphans"""	24829	protein-coding gene	gene with protein product		607234	"""G protein-coupled receptor 169"""	GPR169		12679517	Standard	NM_001164377		Approved	mrgG	uc001lxp.2	Q86SM5	OTTHUMG00000011709	ENST00000332314.3:c.678C>T	11.37:g.3239366G>A		93.0	0.0	0		87.0	49.0	0.563218	NM_001164377		Silent	SNP	ENST00000332314.3	37	CCDS44520.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	MRGPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032347.1		
HIST1H2AE	3012	hgsc.bcm.edu	37	6	26217245	26217245	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26217245G>A	ENST00000303910.2	+	1	81	c.43G>A	c.(43-45)Gct>Act	p.A15T	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	15						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	10		all_hematologic(11;0.196)				TCGGGCAAAAGCTAAAACGCG	0.547																																					p.A15T		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.G43A						PASS	.						66.0	57.0	60.0					6																	26217245		2203	4300	6503	SO:0001583	missense	3012	exon1			GCAAAAGCTAAAA	M60752	CCDS4595.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000168274	ENSG00000277075		"""Histones / Replication-dependent"""	4724	protein-coding gene	gene with protein product		602786	"""H2A histone family, member A"", ""histone 1, H2ae"""	H2AFA		9119399, 1916825, 12408966	Standard	NM_021052		Approved	H2A/a, H2A.1	uc003nha.1	P04908	OTTHUMG00000014440	ENST00000303910.2:c.43G>A	6.37:g.26217245G>A	ENSP00000303373:p.Ala15Thr	89.0	0.0	0		81.0	25.0	0.308642	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	37	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	11.85	1.762076	0.31228	.	.	ENSG00000168274	ENST00000303910	T	0.40756	1.02	3.99	3.99	0.46301	.	0.000000	0.33753	U	0.004582	T	0.49389	0.1554	M	0.69185	2.1	0.48452	D	0.999659	.	.	.	.	.	.	T	0.56257	-0.8009	8	0.87932	D	0	.	15.5885	0.76506	0.0:0.0:1.0:0.0	.	.	.	.	T	15	ENSP00000303373:A15T	ENSP00000303373:A15T	A	+	1	0	HIST1H2AE	26325224	1.000000	0.71417	0.930000	0.37139	0.125000	0.20455	7.595000	0.82710	2.219000	0.72066	0.591000	0.81541	GCT	.	.	none		0.547	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052	
PIM1	5292	hgsc.bcm.edu	37	6	37138946	37138946	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:37138946G>A	ENST00000373509.5	+	4	659	c.286G>A	c.(286-288)Gtg>Atg	p.V96M		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	187					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	GCTGAAGAAGGTGAGCTCGGG	0.652			T	BCL6	NHL																																p.V187M		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G559A						PASS	.						80.0	89.0	86.0					6																	37138946		2203	4300	6503	SO:0001583	missense	5292	exon4			AAGAAGGTGAGCT		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.286G>A	6.37:g.37138946G>A	ENSP00000362608:p.Val96Met	53.0	0.0	0		55.0	8.0	0.145455	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518058	0.85495	.	.	ENSG00000137193	ENST00000373509	T	0.66638	-0.22	4.14	4.14	0.48551	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.077156	0.51477	D	0.000084	T	0.54191	0.1843	N	0.25426	0.745	0.54753	D	0.999985	P	0.37015	0.578	P	0.46076	0.503	T	0.65327	-0.6195	10	0.87932	D	0	.	16.5618	0.84568	0.0:0.0:1.0:0.0	.	187	P11309	PIM1_HUMAN	M	96	ENSP00000362608:V96M	ENSP00000362608:V96M	V	+	1	0	PIM1	37246924	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.549000	0.98106	2.283000	0.76528	0.549000	0.68633	GTG	.	.	none		0.652	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
CACNA1F	778	hgsc.bcm.edu	37	X	49081230	49081230	+	Missense_Mutation	SNP	C	C	T	rs141010716	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49081230C>T	ENST00000376265.2	-	14	1964	c.1903G>A	c.(1903-1905)Gtc>Atc	p.V635I	CACNA1F_ENST00000376251.1_Missense_Mutation_p.V570I|CACNA1F_ENST00000480889.1_5'Flank|CACNA1F_ENST00000323022.5_Missense_Mutation_p.V624I	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	635			V -> I (in CSNB2A; dbSNP:rs141010716). {ECO:0000269|PubMed:12187427}.		axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AACCTGGTGACCTTAAAGATC	0.562													c|||	8	0.00211921	0.0023	0.0	3775	,	,		12808	0.0		0.005	False		,,,				2504	0.0				p.V635I		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G1903A	GRCh37	CM023777	CACNA1F	M	rs141010716	PASS	.		ILE/VAL	4,3806		0,4,0,1623,556	36.0	30.0	32.0		1903	3.4	1.0	X	dbSNP_134	32	22,6662		0,14,8,2408,1832	yes	missense	CACNA1F	NM_005183.2	29	0,18,8,4031,2388	TT,TC,T,CC,C		0.3291,0.105,0.2478	benign	635/1978	49081230	26,10468	2183	4262	6445	SO:0001583	missense	778	exon14			TGGTGACCTTAAA	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.1903G>A	X.37:g.49081230C>T	ENSP00000365441:p.Val635Ile	55.0	0.0	0		69.0	47.0	0.681159	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	5	0.0030138637733574444	2	0.0040650406504065045	0	0.0	0	0.0	2	0.0026455026455026454	.	4.653	0.121374	0.08881	0.00105	0.003291	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98221	-4.8;-4.8;-4.8	3.39	3.39	0.38822	Ion transport (1);	0.501276	0.19185	N	0.120568	D	0.95172	0.8435	L	0.33137	0.985	0.29467	N	0.857304	B;P	0.39216	0.192;0.664	B;B	0.38842	0.094;0.283	D	0.90937	0.4794	10	0.15952	T	0.53	.	13.2338	0.59958	0.0:1.0:0.0:0.0	.	624;635	F5CIQ9;O60840	.;CAC1F_HUMAN	I	570;624;635	ENSP00000365427:V570I;ENSP00000321618:V624I;ENSP00000365441:V635I	ENSP00000321618:V624I	V	-	1	0	CACNA1F	48968174	0.963000	0.33076	1.000000	0.80357	0.222000	0.24845	0.688000	0.25422	1.298000	0.44778	0.273000	0.19326	GTC	C|0.997;T|0.003	0.003	strong		0.562	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
GRIK4	2900	hgsc.bcm.edu	37	11	120531044	120531044	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:120531044C>T	ENST00000527524.2	+	3	304	c.17C>T	c.(16-18)gCg>gTg	p.A6V	GRIK4_ENST00000438375.2_Missense_Mutation_p.A6V	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	6					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.A6V(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		CGCGTCTCGGCGCCTTTGGTG	0.647											OREG0021424	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A6V		Atlas-SNP	.											GRIK4,colon,NS,0,1	GRIK4	149	1	1	Substitution - Missense(1)	large_intestine(1)	c.C17T						PASS	.						70.0	62.0	65.0					11																	120531044		2203	4299	6502	SO:0001583	missense	2900	exon1			TCTCGGCGCCTTT	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.17C>T	11.37:g.120531044C>T	ENSP00000435648:p.Ala6Val	34.0	0.0	0	1504	51.0	20.0	0.392157	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253108	0.59212	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.12465	2.68;2.68	5.55	4.63	0.57726	.	0.000000	0.64402	D	0.000009	T	0.06050	0.0157	N	0.08118	0	0.37509	D	0.917088	P;B	0.34587	0.458;0.102	B;B	0.20184	0.028;0.019	T	0.43589	-0.9382	10	0.20046	T	0.44	.	13.3882	0.60807	0.0:0.9224:0.0:0.0776	.	6;6	A6H8K8;Q16099	.;GRIK4_HUMAN	V	6	ENSP00000435648:A6V;ENSP00000404063:A6V	ENSP00000404063:A6V	A	+	2	0	GRIK4	120036254	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.202000	0.65169	1.467000	0.48044	0.563000	0.77884	GCG	.	.	none		0.647	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11009703C>T	ENST00000377008.4	-	10	1213	c.767G>A	c.(766-768)cGg>cAg	p.R256Q	C1orf127_ENST00000377004.4_Missense_Mutation_p.R423Q			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	256	Pro-rich.		R -> Q (in dbSNP:rs1281012).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		GTCGGAAGGCCGGTGCAGGAG	0.622													C|||	347	0.0692891	0.2042	0.0144	5008	,	,		17273	0.004		0.0427	False		,,,				2504	0.0204				p.R423Q		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1268A						PASS	.	C	GLN/ARG	725,3675		66,593,1541	40.0	34.0	36.0		1268	-6.4	0.0	1	dbSNP_87	36	333,8267		4,325,3971	yes	missense	C1orf127	NM_001170754.1	43	70,918,5512	TT,TC,CC		3.8721,16.4773,8.1385	benign	423/824	11009703	1058,11942	2200	4300	6500	SO:0001583	missense	148345	exon11			GAAGGCCGGTGCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.767G>A	1.37:g.11009703C>T	ENSP00000366207:p.Arg256Gln	61.0	0.0	0		54.0	29.0	0.537037	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	C|C	1.843|1.843	-0.467033|-0.467033	0.04476|0.04476	0.164773|0.164773	0.038721|0.038721	ENSG00000175262|ENSG00000175262	ENST00000418570|ENST00000377004;ENST00000377008	.|T;T	.|0.29142	.|1.58;1.58	3.98|3.98	-6.39|-6.39	0.01951|0.01951	.|.	.|6.202500	.|0.00166	.|N	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18999|0.18999	-1.0319|-1.0319	4|9	.|0.23891	.|T	.|0.37	.|.	2.3424|2.3424	0.04263|0.04263	0.1182:0.3558:0.1181:0.4079|0.1182:0.3558:0.1181:0.4079	rs1281012;rs1281012|rs1281012;rs1281012	.|274;256	.|B7ZLG7;Q8N9H9	.|.;CA127_HUMAN	S|Q	258|423;256	.|ENSP00000366203:R423Q;ENSP00000366207:R256Q	.|ENSP00000366203:R423Q	G|R	-|-	1|2	0|0	C1orf127|C1orf127	10932290|10932290	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.451000|-1.451000	0.02387|0.02387	-1.615000|-1.615000	0.01573|0.01573	-1.314000|-1.314000	0.01303|0.01303	GGC|CGG	C|0.907;T|0.093	0.093	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:15776095C>T	ENST00000281172.5	-	20	2788	c.2352G>A	c.(2350-2352)ttG>ttA	p.L784L	EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000543612.1_Silent_p.L784L|EPS8_ENST00000540613.1_Silent_p.L524L|EPS8_ENST00000542903.1_Silent_p.L524L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	784	Effector region. {ECO:0000250}.|Helix bundle 4. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		GTCATACCTCCAATGCAGCTT	0.418													T|||	882	0.176118	0.5507	0.0562	5008	,	,		17316	0.0536		0.0209	False		,,,				2504	0.0409				p.L784L		Atlas-SNP	.											.	EPS8	70	.	0			c.G2352A						PASS	.	T		2128,2278	599.1+/-389.2	529,1070,604	131.0	135.0	133.0		2352	-0.9	0.7	12	dbSNP_86	133	204,8396	810.5+/-407.1	2,200,4098	no	coding-synonymous	EPS8	NM_004447.5		531,1270,4702	TT,TC,CC		2.3721,48.2978,17.9302		784/823	15776095	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			TACCTCCAATGCA	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2352G>A	12.37:g.15776095C>T		119.0	0.0	0		129.0	63.0	0.488372	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																			T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong		0.418	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1		
SLFN5	162394	hgsc.bcm.edu	37	17	33592323	33592323	+	Missense_Mutation	SNP	C	C	G	rs113644060	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33592323C>G	ENST00000299977.4	+	5	2240	c.2092C>G	c.(2092-2094)Cct>Gct	p.P698A	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	698					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		TGGCCTCCCCCCTCCCTCAGA	0.498													C|||	97	0.019369	0.0265	0.0259	5008	,	,		18966	0.0		0.0179	False		,,,				2504	0.0266				p.P698A		Atlas-SNP	.											.	SLFN5	92	.	0			c.C2092G						PASS	.	C	ALA/PRO	131,4275	95.3+/-134.0	1,129,2073	110.0	108.0	109.0		2092	-6.3	0.0	17	dbSNP_132	109	213,8387	89.4+/-151.6	4,205,4091	yes	missense	SLFN5	NM_144975.3	27	5,334,6164	GG,GC,CC		2.4767,2.9732,2.6449	benign	698/892	33592323	344,12662	2203	4300	6503	SO:0001583	missense	162394	exon5			CTCCCCCCTCCCT	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.2092C>G	17.37:g.33592323C>G	ENSP00000299977:p.Pro698Ala	127.0	0.0	0		140.0	64.0	0.457143	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	37	0.01694139194139194	13	0.026422764227642278	7	0.019337016574585635	0	0.0	17	0.022427440633245383	c	0.035	-1.311433	0.01342	0.029732	0.024767	ENSG00000166750	ENST00000299977	T	0.01804	4.63	3.14	-6.29	0.02013	.	3.015190	0.01558	N	0.019980	T	0.00552	0.0018	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46190	-0.9209	10	0.13108	T	0.6	.	10.9039	0.47069	0.0:0.194:0.6988:0.1073	.	698	Q08AF3	SLFN5_HUMAN	A	698	ENSP00000299977:P698A	ENSP00000299977:P698A	P	+	1	0	SLFN5	30616436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.066000	0.01385	-1.019000	0.03358	-0.259000	0.10710	CCT	C|0.975;G|0.025	0.025	strong		0.498	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
CD27	939	hgsc.bcm.edu	37	12	6554263	6554263	+	Start_Codon_SNP	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6554263T>C	ENST00000266557.3	+	1	231	c.2T>C	c.(1-3)aTg>aCg	p.M1T	CD27-AS1_ENST00000545339.1_RNA|CD27-AS1_ENST00000399492.2_RNA	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	1					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						GCAGGGACCATGGCACGGCCA	0.642																																					p.M1T		Atlas-SNP	.											.	CD27	17	.	0			c.T2C						PASS	.						16.0	22.0	20.0					12																	6554263		2198	4299	6497	SO:0001582	initiator_codon_variant	939	exon1			GGACCATGGCACG	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11922	protein-coding gene	gene with protein product		186711	"""tumor necrosis factor receptor superfamily, member 7"""	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.2T>C	12.37:g.6554263T>C	ENSP00000266557:p.Met1Thr	37.0	0.0	0		25.0	9.0	0.36	NM_001242	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458659	0.43634	.	.	ENSG00000139193	ENST00000266557	D	0.95171	-3.63	4.91	3.7	0.42460	.	0.129490	0.35555	N	0.003121	D	0.93706	0.7989	.	.	.	0.80722	D	1	P	0.51791	0.948	P	0.49528	0.614	D	0.93296	0.6672	9	0.87932	D	0	-14.682	7.8927	0.29688	0.1827:0.0:0.0:0.8173	.	1	P26842	CD27_HUMAN	T	1	ENSP00000266557:M1T	ENSP00000266557:M1T	M	+	2	0	CD27	6424524	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	1.263000	0.33004	2.064000	0.61679	0.455000	0.32223	ATG	.	.	none		0.642	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1		Missense_Mutation
CLCNKA	1187	hgsc.bcm.edu	37	1	16355287	16355287	+	Missense_Mutation	SNP	C	C	G	rs45588635	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16355287C>G	ENST00000331433.4	+	11	1019	c.1000C>G	c.(1000-1002)Ctt>Gtt	p.L334V	CLCNKA_ENST00000375692.1_Missense_Mutation_p.L334V|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.L334V|CLCNKA_ENST00000439316.2_Missense_Mutation_p.L291V			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	334					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GGCCACCTTGCTTCTCGCCTC	0.632													C|||	51	0.0101837	0.0023	0.0101	5008	,	,		15106	0.002		0.0249	False		,,,				2504	0.0143				p.L334V		Atlas-SNP	.											.	CLCNKA	56	.	0			c.C1000G						PASS	.	C	VAL/LEU,VAL/LEU	22,4384	29.0+/-57.7	0,22,2181	197.0	142.0	161.0		1000,1000	-1.2	0.0	1	dbSNP_127	161	258,8342	100.6+/-161.9	7,244,4049	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	32,32	7,266,6230	GG,GC,CC		3.0,0.4993,2.1529	benign,benign	334/687,334/688	16355287	280,12726	2203	4300	6503	SO:0001583	missense	1187	exon11			ACCTTGCTTCTCG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1000C>G	1.37:g.16355287C>G	ENSP00000332771:p.Leu334Val	79.0	0.0	0		61.0	60.0	0.983607	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	28	0.01282051282051282	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	21	0.027704485488126648	C	2.898	-0.228251	0.06022	0.004993	0.03	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	3.37	-1.2	0.09554	Chloride channel, core (2);	0.571234	0.18352	N	0.143854	T	0.62612	0.2442	N	0.12471	0.22	0.30637	N	0.756893	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.16289	0.015;0.015;0.015	T	0.64296	-0.6441	10	0.07644	T	0.81	.	7.6981	0.28606	0.1941:0.5514:0.2544:0.0	rs45588635	291;334;334	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	V	334;334;291;334	ENSP00000364844:L334V;ENSP00000410353:L334V;ENSP00000414445:L291V;ENSP00000332771:L334V	ENSP00000332771:L334V	L	+	1	0	CLCNKA	16227874	0.000000	0.05858	0.003000	0.11579	0.252000	0.25951	-0.757000	0.04772	-0.350000	0.08262	-0.702000	0.03669	CTT	C|0.981;G|0.019	0.019	strong		0.632	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
COL6A5	256076	hgsc.bcm.edu	37	3	130104153	130104153	+	Missense_Mutation	SNP	G	G	A	rs149308947		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:130104153G>A	ENST00000432398.2	+	5	2301	c.1807G>A	c.(1807-1809)Gat>Aat	p.D603N	COL6A5_ENST00000265379.6_Missense_Mutation_p.D603N	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	603	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GCAGAACTTTGATGCTTTGAA	0.388													G|||	1	0.000199681	0.0	0.0	5008	,	,		21518	0.0		0.001	False		,,,				2504	0.0				p.D603N		Atlas-SNP	.											.	COL6A5	205	.	0			c.G1807A						PASS	.						34.0	30.0	31.0					3																	130104153		692	1590	2282	SO:0001583	missense	256076	exon5			AACTTTGATGCTT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.1807G>A	3.37:g.130104153G>A	ENSP00000390895:p.Asp603Asn	75.0	0.0	0		56.0	23.0	0.410714	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.84	3.232744	0.58777	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.79554	-1.28;-1.28	5.28	5.28	0.74379	.	.	.	.	.	D	0.85362	0.5679	L	0.35793	1.09	0.46725	D	0.99917	D	0.89917	1.0	D	0.83275	0.996	D	0.84806	0.0787	9	0.40728	T	0.16	.	17.7195	0.88347	0.0:0.0:1.0:0.0	.	603	A8TX70-2	.	N	603	ENSP00000390895:D603N;ENSP00000265379:D603N	ENSP00000265379:D603N	D	+	1	0	COL6A5	131586843	1.000000	0.71417	0.997000	0.53966	0.395000	0.30598	6.422000	0.73357	2.469000	0.83416	0.557000	0.71058	GAT	G|1.000;A|0.000	0.000	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
GPC6	10082	hgsc.bcm.edu	37	13	94482567	94482567	+	Missense_Mutation	SNP	G	G	A	rs369251626		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:94482567G>A	ENST00000377047.4	+	3	1095	c.480G>A	c.(478-480)atG>atA	p.M160I	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	160					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TGGAGGAAATGCTCAATGACT	0.463																																					p.M160I		Atlas-SNP	.											.	GPC6	102	.	0			c.G480A						PASS	.	G	ILE/MET	0,4406		0,0,2203	116.0	114.0	115.0		480	5.5	1.0	13		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPC6	NM_005708.3	10	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	160/556	94482567	1,13005	2203	4300	6503	SO:0001583	missense	10082	exon3			GGAAATGCTCAAT	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.480G>A	13.37:g.94482567G>A	ENSP00000366246:p.Met160Ile	94.0	0.0	0		127.0	77.0	0.606299	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547215	0.45383	0.0	1.16E-4	ENSG00000183098	ENST00000377047	T	0.51071	0.72	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.47469	0.1447	M	0.65677	2.01	0.33212	D	0.553497	B;B	0.10296	0.002;0.003	B;B	0.18263	0.021;0.012	T	0.53641	-0.8410	10	0.28530	T	0.3	.	14.6399	0.68717	0.0:0.0:0.8545:0.1455	.	160;160	B4E2M1;Q9Y625	.;GPC6_HUMAN	I	160	ENSP00000366246:M160I	ENSP00000366246:M160I	M	+	3	0	GPC6	93280568	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.447000	0.80620	2.775000	0.95449	0.650000	0.86243	ATG	.	.	weak		0.463	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
CSF1R	1436	hgsc.bcm.edu	37	5	149460355	149460355	+	Silent	SNP	G	G	A	rs41287102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149460355G>A	ENST00000286301.3	-	3	573	c.282C>T	c.(280-282)agC>agT	p.S94S	CSF1R_ENST00000543093.1_Silent_p.S94S	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	94	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GGATGGCGGCGCTGCCTCCCA	0.587																																					p.S94S		Atlas-SNP	.											.	CSF1R	250	.	0			c.C282T						PASS	.	G		4,4402	6.2+/-15.9	0,4,2199	73.0	55.0	61.0		282	-9.1	0.0	5	dbSNP_127	61	67,8533	40.8+/-97.7	0,67,4233	no	coding-synonymous	CSF1R	NM_005211.3		0,71,6432	AA,AG,GG		0.7791,0.0908,0.5459		94/973	149460355	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			GGCGGCGCTGCCT	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.282C>T	5.37:g.149460355G>A		149.0	0.0	0		151.0	70.0	0.463576	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.994;A|0.006	0.006	strong		0.587	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
ZNF341	84905	hgsc.bcm.edu	37	20	32376748	32376748	+	Silent	SNP	C	C	T	rs34260449	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32376748C>T	ENST00000375200.1	+	13	2297	c.1932C>T	c.(1930-1932)caC>caT	p.H644H	RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|ZNF341_ENST00000342427.2_Silent_p.H637H|RP4-553F4.6_ENST00000443171.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						TGTTGATCCACGAGCCCTTCA	0.552													C|||	60	0.0119808	0.0	0.0159	5008	,	,		17759	0.001		0.0318	False		,,,				2504	0.0164				p.H637H		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1911T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	121.0	99.0	106.0		1911	-4.3	1.0	20	dbSNP_126	106	180,8420	82.6+/-145.2	2,176,4122	no	coding-synonymous	ZNF341	NM_032819.3		2,193,6308	TT,TC,CC		2.093,0.3858,1.5147		637/848	32376748	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GATCCACGAGCCC	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1932C>T	20.37:g.32376748C>T		180.0	0.0	0		142.0	75.0	0.528169	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.985;T|0.015	0.015	strong		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
CDCA4	55038	hgsc.bcm.edu	37	14	105478159	105478159	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105478159C>T	ENST00000336219.3	-	2	263	c.108G>A	c.(106-108)tcG>tcA	p.S36S	CDCA4_ENST00000392590.3_Silent_p.S36S	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	36	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)		TGTCCAGGAGCGACTGCCGCT	0.592																																					p.S36S		Atlas-SNP	.											.	CDCA4	18	.	0			c.G108A						PASS	.						71.0	59.0	63.0					14																	105478159		2203	4300	6503	SO:0001819	synonymous_variant	55038	exon2			CAGGAGCGACTGC	BG354577	CCDS9996.1	14q32.33	2014-02-14			ENSG00000170779	ENSG00000170779			14625	protein-coding gene	gene with protein product	"""hematopoietic progenitor protein"""	612270				12188893	Standard	NM_145701		Approved	FLJ20764, Hepp	uc001yqb.2	Q9BXL8	OTTHUMG00000170767	ENST00000336219.3:c.108G>A	14.37:g.105478159C>T		57.0	0.0	0		80.0	33.0	0.4125	NM_017955	Q8TB18|Q9NWK7	Silent	SNP	ENST00000336219.3	37	CCDS9996.1																																																																																			.	.	none		0.592	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701	
PSME4	23198	hgsc.bcm.edu	37	2	54161756	54161756	+	Missense_Mutation	SNP	T	T	C	rs146618010		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54161756T>C	ENST00000404125.1	-	8	998	c.943A>G	c.(943-945)Atc>Gtc	p.I315V	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	315					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ATGGCGGTGATCCATATTACA	0.363																																					p.I315V		Atlas-SNP	.											.	PSME4	247	.	0			c.A943G						PASS	.	T	VAL/ILE	0,4406		0,0,2203	101.0	101.0	101.0		943	4.5	1.0	2	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PSME4	NM_014614.2	29	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	315/1844	54161756	1,13005	2203	4300	6503	SO:0001583	missense	23198	exon8			CGGTGATCCATAT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.943A>G	2.37:g.54161756T>C	ENSP00000384211:p.Ile315Val	65.0	0.0	0		53.0	22.0	0.415094	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322036	0.41096	0.0	1.16E-4	ENSG00000068878	ENST00000404125	T	0.06294	3.32	5.64	4.49	0.54785	.	0.051963	0.85682	D	0.000000	T	0.09686	0.0238	M	0.73217	2.22	0.80722	D	1	B	0.30542	0.284	B	0.31290	0.127	T	0.08432	-1.0722	10	0.24483	T	0.36	.	11.5732	0.50845	0.0:0.0697:0.0:0.9303	.	315	Q14997	PSME4_HUMAN	V	315	ENSP00000384211:I315V	ENSP00000374643:I315V	I	-	1	0	PSME4	54015260	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.789000	0.47813	1.078000	0.41014	0.482000	0.46254	ATC	T|1.000;C|0.000	0.000	weak		0.363	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
PLXNB3	5365	hgsc.bcm.edu	37	X	153043896	153043896	+	Silent	SNP	G	G	A	rs144872102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153043896G>A	ENST00000361971.5	+	34	5634	c.5520G>A	c.(5518-5520)gaG>gaA	p.E1840E	SRPK3_ENST00000370104.1_5'Flank|SRPK3_ENST00000370108.3_5'Flank|SRPK3_ENST00000370100.1_5'Flank|SRPK3_ENST00000370101.3_5'Flank|PLXNB3_ENST00000538776.1_Silent_p.E1493E|SRPK3_ENST00000393786.3_5'Flank|PLXNB3_ENST00000538966.1_Silent_p.E1863E|SRPK3_ENST00000489426.1_De_novo_Start_OutOfFrame	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1840					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GCTACCAGGAGATGAACTCTG	0.647													G|||	2	0.000529801	0.0	0.0	3775	,	,		13514	0.0		0.002	False		,,,				2504	0.0				p.E1863E		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G5589A						PASS	.	G	,	1,3834		0,1,0,1631,571	43.0	41.0	42.0		5589,5520	2.4	1.0	X	dbSNP_134	42	8,6720		0,5,3,2423,1869	no	coding-synonymous,coding-synonymous	PLXNB3	NM_001163257.1,NM_005393.2	,	0,6,3,4054,2440	AA,AG,A,GG,G		0.1189,0.0261,0.0852	,	1863/1933,1840/1910	153043896	9,10554	2203	4300	6503	SO:0001819	synonymous_variant	5365	exon35			CCAGGAGATGAAC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.5520G>A	X.37:g.153043896G>A		62.0	0.0	0		76.0	47.0	0.618421	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1																																																																																			G|0.999;A|0.001	0.001	strong		0.647	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
WDR72	256764	hgsc.bcm.edu	37	15	54007512	54007512	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:54007512C>A	ENST00000396328.1	-	5	631	c.392G>T	c.(391-393)gGa>gTa	p.G131V	WDR72_ENST00000360509.5_Missense_Mutation_p.G131V|WDR72_ENST00000557913.1_Missense_Mutation_p.G131V|WDR72_ENST00000559418.1_Missense_Mutation_p.G131V	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	131										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		TTGATATTCTCCACAACAAAG	0.378																																					p.G131V		Atlas-SNP	.											.	WDR72	177	.	0			c.G392T						PASS	.						92.0	89.0	90.0					15																	54007512		2194	4293	6487	SO:0001583	missense	256764	exon5			TATTCTCCACAAC	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.392G>T	15.37:g.54007512C>A	ENSP00000379619:p.Gly131Val	223.0	0.0	0		223.0	64.0	0.286996	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410211	0.83340	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.64803	-0.12;-0.12	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.80670	0.4667	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82526	-0.0413	10	0.87932	D	0	.	18.5785	0.91163	0.0:1.0:0.0:0.0	.	131	Q3MJ13	WDR72_HUMAN	V	131	ENSP00000379619:G131V;ENSP00000353699:G131V	ENSP00000353699:G131V	G	-	2	0	WDR72	51794804	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.640000	0.74319	2.629000	0.89072	0.655000	0.94253	GGA	.	.	none		0.378	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
ARID4A	5926	hgsc.bcm.edu	37	14	58831258	58831258	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:58831258A>C	ENST00000355431.3	+	20	2824	c.2451A>C	c.(2449-2451)gcA>gcC	p.A817A	ARID4A_ENST00000348476.3_Silent_p.A817A|ARID4A_ENST00000395168.3_Silent_p.A817A|ARID4A_ENST00000431317.2_Silent_p.A817A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	817					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AGAATGAAGCAGGAAGTGAAC	0.343																																					p.A817A		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2451C						PASS	.						39.0	44.0	42.0					14																	58831258		2198	4295	6493	SO:0001819	synonymous_variant	5926	exon20			TGAAGCAGGAAGT	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2451A>C	14.37:g.58831258A>C		87.0	0.0	0		85.0	16.0	0.188235	NM_002892	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																			.	.	none		0.343	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
CHML	1122	hgsc.bcm.edu	37	1	241797585	241797585	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:241797585C>G	ENST00000366553.1	-	1	1647	c.1484G>C	c.(1483-1485)tGt>tCt	p.C495S	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	495					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GGTTGAAGAACATAATTCTGT	0.413																																					p.C495S		Atlas-SNP	.											.	CHML	82	.	0			c.G1484C						PASS	.						92.0	87.0	89.0					1																	241797585		2203	4299	6502	SO:0001583	missense	1122	exon1			GAAGAACATAATT	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1484G>C	1.37:g.241797585C>G	ENSP00000355511:p.Cys495Ser	86.0	0.0	0		90.0	47.0	0.522222	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.762053	0.31228	.	.	ENSG00000203668	ENST00000366553	T	0.76448	-1.02	5.08	5.08	0.68730	.	0.047679	0.85682	U	0.000000	T	0.62221	0.2410	.	.	.	0.58432	D	0.99999	B	0.25667	0.131	B	0.31751	0.135	T	0.57487	-0.7803	9	0.02654	T	1	-4.293	16.3808	0.83460	0.0:1.0:0.0:0.0	.	495	P26374	RAE2_HUMAN	S	495	ENSP00000355511:C495S	ENSP00000355511:C495S	C	-	2	0	CHML	239864208	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.326000	0.52037	2.826000	0.97356	0.655000	0.94253	TGT	.	.	none		0.413	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
ATRNL1	26033	hgsc.bcm.edu	37	10	117061434	117061434	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:117061434C>T	ENST00000355044.3	+	17	2825	c.2699C>T	c.(2698-2700)aCa>aTa	p.T900I	ATRNL1_ENST00000423111.2_5'UTR|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	900	PSI 4.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TCCAACTGTACAAGCAATGGC	0.403																																					p.T900I		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C2699T						PASS	.						246.0	175.0	199.0					10																	117061434		2203	4300	6503	SO:0001583	missense	26033	exon17			ACTGTACAAGCAA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2699C>T	10.37:g.117061434C>T	ENSP00000347152:p.Thr900Ile	97.0	0.0	0		107.0	24.0	0.224299	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423342	0.83559	.	.	ENSG00000107518	ENST00000355044	T	0.15256	2.44	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.19128	-1.0315	10	0.56958	D	0.05	-15.0727	19.0195	0.92908	0.0:1.0:0.0:0.0	.	900	Q5VV63	ATRN1_HUMAN	I	900	ENSP00000347152:T900I	ENSP00000347152:T900I	T	+	2	0	ATRNL1	117051424	1.000000	0.71417	0.688000	0.30117	0.983000	0.72400	7.730000	0.84881	2.491000	0.84063	0.591000	0.81541	ACA	.	.	none		0.403	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
WHSC1	7468	hgsc.bcm.edu	37	4	1957774	1957774	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:1957774G>A	ENST00000382895.3	+	17	3171	c.2740G>A	c.(2740-2742)Gag>Aag	p.E914K	WHSC1_ENST00000508803.1_Missense_Mutation_p.E914K|WHSC1_ENST00000382888.3_Missense_Mutation_p.E262K|WHSC1_ENST00000382892.2_Missense_Mutation_p.E914K|WHSC1_ENST00000382891.5_Missense_Mutation_p.E914K|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	914	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		AATGAAGCACGAGATTGGAGA	0.463			T	IGH@	MM																																p.E914K		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.G2740A						PASS	.						144.0	171.0	162.0					4																	1957774		2203	4300	6503	SO:0001583	missense	7468	exon15			AAGCACGAGATTG	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2740G>A	4.37:g.1957774G>A	ENSP00000372351:p.Glu914Lys	109.0	0.0	0		93.0	4.0	0.0430108	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.141559|5.141559	0.94560|0.94560	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888|ENST00000514329	T;T;T;T;T|.	0.69306|.	-0.39;-0.39;-0.39;-0.39;-0.39|.	5.97|5.97	5.97|5.97	0.96955|0.96955	PWWP (3);|.	0.000000|.	0.64402|.	D|.	0.000016|.	T|T	0.51702|0.51702	0.1690|0.1690	N|N	0.12887|0.12887	0.27|0.27	0.80722|0.80722	D|D	1|1	P;D|.	0.76494|.	0.615;0.999|.	B;P|.	0.56700|.	0.227;0.804|.	T|T	0.44097|0.44097	-0.9350|-0.9350	10|5	0.22109|.	T|.	0.4|.	.|.	20.4387|20.4387	0.99107|0.99107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	262;914|.	A2A2T2;O96028|.	.;NSD2_HUMAN|.	K|Q	914;914;914;914;262|237	ENSP00000423972:E914K;ENSP00000372347:E914K;ENSP00000372348:E914K;ENSP00000372351:E914K;ENSP00000372344:E262K|.	ENSP00000372344:E262K|.	E|R	+|+	1|2	0|0	WHSC1|WHSC1	1927572|1927572	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.562000|6.562000	0.73960|0.73960	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.	none		0.463	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
ZNRF3	84133	hgsc.bcm.edu	37	22	29445817	29445817	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29445817G>A	ENST00000544604.2	+	8	1823	c.1648G>A	c.(1648-1650)Gac>Aac	p.D550N	ZNRF3_ENST00000332811.4_Missense_Mutation_p.D450N|ZNRF3_ENST00000406323.3_Missense_Mutation_p.D450N|ZNRF3_ENST00000402174.1_Missense_Mutation_p.D450N	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	550					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CCCAGgcagcgacagcagcag	0.662																																					p.D550N		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G1648A						PASS	.						14.0	17.0	16.0					22																	29445817		1965	3949	5914	SO:0001583	missense	84133	exon8			GGCAGCGACAGCA	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1648G>A	22.37:g.29445817G>A	ENSP00000443824:p.Asp550Asn	110.0	0.0	0		86.0	27.0	0.313953	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	37	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650547	0.87958	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.44	5.44	0.79542	.	0.289400	0.41712	D	0.000829	D	0.88672	0.6500	M	0.61703	1.905	0.52501	D	0.999951	D	0.89917	1.0	D	0.85130	0.997	D	0.89083	0.3477	10	0.62326	D	0.03	-1.1774	18.24	0.89965	0.0:0.0:1.0:0.0	.	550	Q9ULT6	ZNRF3_HUMAN	N	550;450;257;450;450	ENSP00000443824:D550N;ENSP00000328614:D450N;ENSP00000384456:D450N;ENSP00000384553:D450N	ENSP00000328614:D450N	D	+	1	0	ZNRF3	27775817	1.000000	0.71417	0.999000	0.59377	0.844000	0.47949	9.357000	0.97099	2.546000	0.85860	0.655000	0.94253	GAC	.	.	none		0.662	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972	
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56505175T>A	ENST00000361203.3	-	14	1630	c.1623A>T	c.(1621-1623)tcA>tcT	p.S541S	DST_ENST00000370769.4_Silent_p.S541S|DST_ENST00000518935.1_Silent_p.S215S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370788.2_Silent_p.S541S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000446842.2_Silent_p.S215S			Q03001	DYST_HUMAN	dystonin	541					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGTCATCCCTGATGACAGGC	0.483													T|||	11	0.00219649	0.0	0.0	5008	,	,		18999	0.0		0.005	False		,,,				2504	0.0061				p.S215S		Atlas-SNP	.											.	DST	1427	.	0			c.A645T						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	139.0	141.0	141.0		645,645	-4.8	0.6	6	dbSNP_132	141	36,8564	25.1+/-72.6	0,36,4264	yes	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,40,6463	AA,AT,TT		0.4186,0.0908,0.3076	,	215/2650,215/5172	56505175	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			CATCCCTGATGAC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1623A>T	6.37:g.56505175T>A		136.0	0.0	0		132.0	70.0	0.530303	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				T|0.997;A|0.003	0.003	strong		0.483	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
ZNF81	347344	hgsc.bcm.edu	37	X	47774599	47774599	+	Missense_Mutation	SNP	C	C	T	rs186251256		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47774599C>T	ENST00000376954.1	+	6	922	c.554C>T	c.(553-555)tCa>tTa	p.S185L	ZNF81_ENST00000338637.7_Missense_Mutation_p.S185L			P51508	ZNF81_HUMAN	zinc finger protein 81	185			S -> L (in dbSNP:rs186251256). {ECO:0000269|PubMed:15121780}.		regulation of transcription, DNA-templated (GO:0006355)|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)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				CTCATTCTTTCACAGAAAAGA	0.328													C|||	17	0.00450331	0.0	0.0058	3775	,	,		14189	0.0		0.0129	False		,,,				2504	0.0				p.S185L		Atlas-SNP	.											.	ZNF81	60	.	0			c.C554T						PASS	.	C	LEU/SER	8,3049		0,7,1,1237,568	40.0	36.0	38.0		554	3.2	1.0	X		38	104,6250		0,78,26,2215,1742	yes	missense	ZNF81	NM_007137.3	145	0,85,27,3452,2310	TT,TC,T,CC,C		1.6368,0.2617,1.1901	probably-damaging	185/662	47774599	112,9299	1813	4061	5874	SO:0001583	missense	347344	exon5			TTCTTTCACAGAA	AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"""Zinc fingers, C2H2-type"", ""-"""	13156	protein-coding gene	gene with protein product		314998	"""zinc finger protein 81 (HFZ20)"", ""mental retardation, X-linked 45"""	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.554C>T	X.37:g.47774599C>T	ENSP00000366153:p.Ser185Leu	198.0	0.0	0		279.0	197.0	0.706093	NM_007137	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	14	0.008438818565400843	0	0.0	4	0.011049723756906077	0	0.0	10	0.013227513227513227	C	15.24	2.774871	0.49786	0.002617	0.016368	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.06068	3.35;3.35	4.04	3.18	0.36537	.	0.228496	0.22784	N	0.055692	T	0.02083	0.0065	N	0.21448	0.665	0.29252	N	0.871902	B	0.18610	0.029	B	0.15484	0.013	T	0.20840	-1.0263	10	0.39692	T	0.17	.	9.0083	0.36127	0.0:0.8864:0.0:0.1136	.	185	P51508	ZNF81_HUMAN	L	185	ENSP00000366153:S185L;ENSP00000341151:S185L	ENSP00000341151:S185L	S	+	2	0	ZNF81	47659543	0.000000	0.05858	0.973000	0.42090	0.625000	0.37756	-0.284000	0.08422	1.067000	0.40740	0.600000	0.82982	TCA	C|0.992;T|0.008	0.008	strong		0.328	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137	
RANBP6	26953	hgsc.bcm.edu	37	9	6012347	6012347	+	Silent	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6012347T>A	ENST00000259569.5	-	1	3271	c.3261A>T	c.(3259-3261)gtA>gtT	p.V1087V	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	1087					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CAAGTTGTGATACACATTCCA	0.353																																					p.V1087V		Atlas-SNP	.											.	RANBP6	127	.	0			c.A3261T						PASS	.						78.0	73.0	74.0					9																	6012347		2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TTGTGATACACAT	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.3261A>T	9.37:g.6012347T>A		81.0	0.0	0		79.0	29.0	0.367089	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																			.	.	none		0.353	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
CXCL14	9547	hgsc.bcm.edu	37	5	134914455	134914455	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134914455G>A	ENST00000337225.5	-	1	514	c.50C>T	c.(49-51)gCg>gTg	p.A17V	CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.A5V|CTC-321K16.1_ENST00000514446.1_RNA	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	17					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inner ear development (GO:0048839)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	chemokine activity (GO:0008009)			large_intestine(2)|lung(2)|prostate(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAGCGCGGCCGCCAGGAGCCT	0.736																																					p.A17V		Atlas-SNP	.											.	CXCL14	13	.	0			c.C50T						PASS	.						7.0	7.0	7.0					5																	134914455		1872	3636	5508	SO:0001583	missense	9547	exon1			GCGGCCGCCAGGA	AF073957	CCDS4188.1	5q31	2010-04-30	2002-08-22	2002-08-23	ENSG00000145824	ENSG00000145824			10640	protein-coding gene	gene with protein product	"""breast and kidney"""	604186	"""small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK)"""	SCYB14		10049774	Standard	NM_004887		Approved	BRAK, NJAC, bolekine, Kec, MIP-2g, BMAC, KS1	uc003lay.3	O95715	OTTHUMG00000129139	ENST00000337225.5:c.50C>T	5.37:g.134914455G>A	ENSP00000337065:p.Ala17Val	52.0	0.0	0		23.0	7.0	0.304348	NM_004887	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	ENST00000337225.5	37	CCDS4188.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715059	0.48622	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	.	.	.	4.67	2.87	0.33458	.	0.397487	0.29355	N	0.012388	T	0.17534	0.0421	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.15752	-1.0426	9	0.42905	T	0.14	12.4482	7.9254	0.29872	0.0825:0.0:0.7596:0.1579	.	17	O95715	CXL14_HUMAN	V	17;5	.	ENSP00000337065:A17V	A	-	2	0	CXCL14	134942354	0.997000	0.39634	0.016000	0.15963	0.994000	0.84299	3.004000	0.49513	0.404000	0.25506	0.563000	0.77884	GCG	.	.	none		0.736	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004887	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735361	140735361	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140735361C>T	ENST00000571252.1	+	1	594	c.594C>T	c.(592-594)cgC>cgT	p.R198R	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	198	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGAACGCGCTCTAGATC	0.567																																					p.R198R		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.C594T						PASS	.						27.0	30.0	29.0					5																	140735361		2160	4285	6445	SO:0001819	synonymous_variant	56111	exon1			GGAACGCGCTCTA	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.594C>T	5.37:g.140735361C>T		80.0	0.0	0		72.0	31.0	0.430556	NM_018917	Q9Y5D3	Silent	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.	.	none		0.567	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
C6orf118	168090	hgsc.bcm.edu	37	6	165715405	165715405	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:165715405C>T	ENST00000230301.8	-	2	426	c.406G>A	c.(406-408)Gcc>Acc	p.A136T	C6orf118_ENST00000543069.1_Missense_Mutation_p.A32T	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	136										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		GAAAGAGAGGCCTGGGGGTTC	0.627																																					p.A136T		Atlas-SNP	.											.	C6orf118	116	.	0			c.G406A						PASS	.						66.0	74.0	71.0					6																	165715405		2203	4299	6502	SO:0001583	missense	168090	exon2			GAGAGGCCTGGGG		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.406G>A	6.37:g.165715405C>T	ENSP00000230301:p.Ala136Thr	28.0	0.0	0		29.0	9.0	0.310345	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904170	0.33628	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.15017	2.68;2.46	4.9	-3.28	0.05033	.	0.915788	0.09168	N	0.839280	T	0.02767	0.0083	L	0.34521	1.04	0.09310	N	1	B	0.24721	0.11	B	0.21151	0.033	T	0.44097	-0.9350	10	0.28530	T	0.3	.	2.3892	0.04374	0.1184:0.163:0.4086:0.3101	.	136	Q5T5N4	CF118_HUMAN	T	136;32	ENSP00000230301:A136T;ENSP00000439288:A32T	ENSP00000230301:A136T	A	-	1	0	C6orf118	165635395	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-3.014000	0.00646	-0.308000	0.08792	0.655000	0.94253	GCC	.	.	none		0.627	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
MGA	23269	hgsc.bcm.edu	37	15	41988709	41988709	+	Missense_Mutation	SNP	A	A	G	rs199666635		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41988709A>G	ENST00000570161.1	+	2	1501	c.1501A>G	c.(1501-1503)Atg>Gtg	p.M501V	MGA_ENST00000566586.1_Missense_Mutation_p.M501V|MGA_ENST00000219905.7_Missense_Mutation_p.M501V|MGA_ENST00000389936.4_Missense_Mutation_p.M501V|MGA_ENST00000568630.1_3'UTR|MGA_ENST00000545763.1_Missense_Mutation_p.M501V			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TAAATCTTCTATGTTGGCAGA	0.403																																					p.M501V		Atlas-SNP	.											.	MGA	264	.	0			c.A1501G						PASS	.	A	VAL/MET,VAL/MET	0,3680		0,0,1840	78.0	73.0	74.0		1501,1501	-8.1	0.0	15		74	5,8175		0,5,4085	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	21,21	0,5,5925	GG,GA,AA		0.0611,0.0,0.0422	benign,benign	501/2857,501/3066	41988709	5,11855	1840	4090	5930	SO:0001583	missense	23269	exon3			TCTTCTATGTTGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1501A>G	15.37:g.41988709A>G	ENSP00000457035:p.Met501Val	63.0	0.0	0		40.0	28.0	0.7	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	3.281	-0.146993	0.06627	0.0	6.11E-4	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.82526	-1.61;-1.62;-1.61	4.53	-8.14	0.01069	.	1.679160	0.03077	N	0.157995	T	0.56426	0.1984	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53049	-0.8493	10	0.21540	T	0.41	.	2.9361	0.05815	0.5423:0.1875:0.1432:0.127	.	501;501	F5H7K2;E7ENI0	.;.	V	501	ENSP00000219905:M501V;ENSP00000374586:M501V;ENSP00000442467:M501V	ENSP00000219905:M501V	M	+	1	0	MGA	39776001	0.002000	0.14202	0.006000	0.13384	0.986000	0.74619	-0.997000	0.03705	-2.196000	0.00751	0.379000	0.24179	ATG	.	.	weak		0.403	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
CIITA	4261	hgsc.bcm.edu	37	16	11001256	11001256	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11001256C>T	ENST00000324288.8	+	11	2040	c.1907C>T	c.(1906-1908)aCg>aTg	p.T636M	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	636	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CTGCCCTCCACGCTCACGGGA	0.692			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.T636M		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.C1907T						PASS	.						21.0	21.0	21.0					16																	11001256		2197	4295	6492	SO:0001583	missense	4261	exon11			CCTCCACGCTCAC	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1907C>T	16.37:g.11001256C>T	ENSP00000316328:p.Thr636Met	121.0	0.0	0		105.0	41.0	0.390476	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.875438	0.51695	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	D	0.81821	-1.54	5.1	5.1	0.69264	NACHT nucleoside triphosphatase (1);	0.000000	0.56097	D	0.000031	D	0.91264	0.7246	M	0.88979	2.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	D	0.92957	0.6385	10	0.87932	D	0	.	17.076	0.86586	0.0:1.0:0.0:0.0	.	636;636;588;636	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	M	636;588	ENSP00000316328:T636M	ENSP00000316328:T636M	T	+	2	0	CIITA	10908757	0.989000	0.36119	0.919000	0.36401	0.068000	0.16541	5.680000	0.68168	2.372000	0.80975	0.655000	0.94253	ACG	.	.	none		0.692	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
DNAH8	1769	hgsc.bcm.edu	37	6	38690860	38690860	+	5'Flank	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38690860C>T	ENST00000359357.3	+	0	0				DNAH8_ENST00000449981.2_Missense_Mutation_p.P92L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCACCGCGACCGGTTCAGTCA	0.517																																					p.P92L		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C275T						PASS	.						109.0	99.0	102.0					6																	38690860		876	1991	2867	SO:0001631	upstream_gene_variant	1769	exon2			CGCGACCGGTTCA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253		6.37:g.38690860C>T	Exception_encountered	90.0	0.0	0		107.0	30.0	0.280374	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	C	10.77	1.444543	0.25987	.	.	ENSG00000124721	ENST00000373278;ENST00000449981;ENST00000327475	T	0.24723	1.84	5.79	0.29	0.15728	.	0.458105	0.20852	N	0.084504	T	0.03783	0.0107	N	0.19112	0.55	0.19300	N	0.999974	B	0.14805	0.011	B	0.09377	0.004	T	0.39057	-0.9632	10	0.32370	T	0.25	.	3.1541	0.06498	0.137:0.5428:0.1346:0.1856	.	92	Q8IU65	.	L	92;80;80	ENSP00000333363:P80L	ENSP00000333363:P80L	P	+	2	0	DNAH8	38798838	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.138000	0.10374	0.015000	0.14971	0.561000	0.74099	CCG	.	.	none		0.517	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
CAND1	55832	hgsc.bcm.edu	37	12	67699536	67699536	+	Silent	SNP	G	G	A	rs17781675	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:67699536G>A	ENST00000545606.1	+	10	2525	c.2088G>A	c.(2086-2088)gaG>gaA	p.E696E		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	696					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TTCTAGATGAGCTCCCACCTC	0.408													G|||	137	0.0273562	0.0159	0.0605	5008	,	,		21008	0.0		0.0586	False		,,,				2504	0.0153				p.E696E		Atlas-SNP	.											.	CAND1	100	.	0			c.G2088A						PASS	.	G		91,4315	76.2+/-114.5	2,87,2114	109.0	105.0	106.0		2088	5.8	1.0	12	dbSNP_123	106	487,8113	141.7+/-198.0	9,469,3822	no	coding-synonymous	CAND1	NM_018448.3		11,556,5936	AA,AG,GG		5.6628,2.0654,4.4441		696/1231	67699536	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			AGATGAGCTCCCA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.2088G>A	12.37:g.67699536G>A		58.0	0.0	0		56.0	22.0	0.392857	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																			G|0.959;A|0.041	0.041	strong		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:146993715G>T	ENST00000370475.4	+	1	146	c.18G>T	c.(16-18)gtG>gtT	p.V6V	FMR1_ENST00000334557.6_Silent_p.V6V|FMR1-AS1_ENST00000598667.1_RNA|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000370470.1_Silent_p.V6V|FMR1_ENST00000370471.3_Silent_p.V6V|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000218200.8_Silent_p.V6V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	6	Agenet-like 1.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTGGTGGTGGAAGTGCGGG	0.677									Fragile X syndrome				G|||	15	0.00397351	0.0	0.0029	3775	,	,		5155	0.0		0.0129	False		,,,				2504	0.0				p.V6V		Atlas-SNP	.											.	FMR1	93	.	0			c.G18T						PASS	.	G	,,,,	6,3525		0,6,0,1538,443	76.0	50.0	59.0		18,18,18,18,18	4.0	1.0	X	dbSNP_132	59	79,6026		0,62,17,2208,1548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	0,68,17,3746,1991	TT,TG,T,GG,G		1.294,0.1699,0.8821	,,,,	6/538,6/612,6/517,6/587,6/633	146993715	85,9551	1987	3835	5822	SO:0001819	synonymous_variant	2332	exon1	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	GGTGGTGGAAGTG	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.18G>T	X.37:g.146993715G>T		89.0	0.0	0		123.0	27.0	0.219512	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			C|0.000;G|0.987;T|0.013	0.013	strong		0.677	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
EP400	57634	hgsc.bcm.edu	37	12	132528724	132528724	+	Silent	SNP	C	C	T	rs61944617	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132528724C>T	ENST00000333577.4	+	36	6670	c.6561C>T	c.(6559-6561)gaC>gaT	p.D2187D	EP400_ENST00000389561.2_Silent_p.D2151D|EP400_ENST00000330386.6_Silent_p.D2070D|EP400_ENST00000332482.4_Silent_p.D2114D|EP400_ENST00000389562.2_Silent_p.D2150D			Q96L91	EP400_HUMAN	E1A binding protein p400	2187					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCGTCAGGACGCAGTGATGA	0.627													c|||	28	0.00559105	0.0	0.0086	5008	,	,		18518	0.0		0.003	False		,,,				2504	0.0194				p.D2151D		Atlas-SNP	.											.	EP400	370	.	0			c.C6453T						PASS	.	T		3,4403	9.9+/-24.2	0,3,2200	55.0	54.0	54.0		6453	-10.6	0.0	12	dbSNP_129	54	45,8555	29.0+/-79.6	0,45,4255	no	coding-synonymous	EP400	NM_015409.4		0,48,6455	TT,TC,CC		0.5233,0.0681,0.3691		2151/3124	132528724	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon35			TCAGGACGCAGTG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.6561C>T	12.37:g.132528724C>T		70.0	0.0	0		74.0	43.0	0.581081	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.996;T|0.004	0.004	strong		0.627	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
TCF12	6938	hgsc.bcm.edu	37	15	57565432	57565432	+	Silent	SNP	C	C	T	rs77034126	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:57565432C>T	ENST00000267811.5	+	18	2182	c.1878C>T	c.(1876-1878)gtC>gtT	p.V626V	TCF12_ENST00000559703.1_Silent_p.V283V|TCF12_ENST00000452095.2_Silent_p.V646V|TCF12_ENST00000537840.1_Silent_p.V390V|TCF12_ENST00000557843.1_Silent_p.V626V|TCF12_ENST00000343827.3_Silent_p.V456V|TCF12_ENST00000543579.1_Silent_p.V480V|TCF12_ENST00000559710.1_Silent_p.V260V|TCF12_ENST00000333725.5_Silent_p.V650V|TCF12_ENST00000438423.2_Silent_p.V650V	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	626	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CCGTGGCAGTCATCCTTAGTC	0.428			T	TEC	extraskeletal myxoid chondrosarcoma								C|||	13	0.00259585	0.0008	0.0086	5008	,	,		20548	0.0		0.006	False		,,,				2504	0.0				p.V650V		Atlas-SNP	.		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	.	TCF12	242	.	0			c.C1950T						PASS	.	C	,,,,	7,4377	12.9+/-30.5	0,7,2185	88.0	84.0	85.0		1878,1950,1950,1878,1368	4.8	1.0	15	dbSNP_131	85	52,8532	33.8+/-87.4	0,52,4240	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF12	NM_003205.3,NM_207036.1,NM_207037.1,NM_207038.1,NM_207040.1	,,,,	0,59,6425	TT,TC,CC		0.6058,0.1597,0.455	,,,,	626/683,650/707,650/707,626/683,456/513	57565432	59,12909	2192	4292	6484	SO:0001819	synonymous_variant	6938	exon19			GGCAGTCATCCTT	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1878C>T	15.37:g.57565432C>T		127.0	0.0	0		121.0	61.0	0.504132	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																			C|0.996;T|0.004	0.004	strong		0.428	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358837	21358837	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:21358837T>G	ENST00000256958.2	+	11	1463	c.1367T>G	c.(1366-1368)cTt>cGt	p.L456R		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	456	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GATGTACCACTTTCTTATTGC	0.383																																					p.L456R		Atlas-SNP	.											SLCO1B1,right_lower_lobe,carcinoma,+1,1	SLCO1B1	151	1	0			c.T1367G						PASS	.						116.0	112.0	113.0					12																	21358837		2203	4300	6503	SO:0001583	missense	10599	exon11			TACCACTTTCTTA		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1367T>G	12.37:g.21358837T>G	ENSP00000256958:p.Leu456Arg	91.0	0.0	0		94.0	22.0	0.234043	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	T	8.595	0.885569	0.17540	.	.	ENSG00000134538	ENST00000256958	T	0.41400	1.0	4.06	2.91	0.33838	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.34828	N	0.003645	T	0.44561	0.1299	M	0.76328	2.33	0.27666	N	0.946908	P	0.35793	0.521	B	0.42163	0.378	T	0.42932	-0.9422	10	0.52906	T	0.07	.	5.5666	0.17175	0.0:0.2326:0.0:0.7674	.	456	Q9Y6L6	SO1B1_HUMAN	R	456	ENSP00000256958:L456R	ENSP00000256958:L456R	L	+	2	0	SLCO1B1	21250104	0.998000	0.40836	0.997000	0.53966	0.557000	0.35523	1.733000	0.38156	0.437000	0.26423	0.397000	0.26171	CTT	.	.	none		0.383	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
RP1	6101	hgsc.bcm.edu	37	8	55538741	55538741	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:55538741A>G	ENST00000220676.1	+	4	2447	c.2299A>G	c.(2299-2301)Aat>Gat	p.N767D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	767					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TACTACTCAAAATTCCAAGGT	0.284																																					p.N767D	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A2299G						PASS	.						23.0	27.0	25.0					8																	55538741		2155	4271	6426	SO:0001583	missense	6101	exon4			ACTCAAAATTCCA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2299A>G	8.37:g.55538741A>G	ENSP00000220676:p.Asn767Asp	53.0	0.0	0		44.0	17.0	0.386364	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	11.03	1.520141	0.27211	.	.	ENSG00000104237	ENST00000220676	T	0.25250	1.81	5.93	5.93	0.95920	.	0.438446	0.21621	N	0.071658	T	0.27900	0.0687	L	0.56769	1.78	0.09310	N	1	B	0.21381	0.055	B	0.20955	0.032	T	0.22173	-1.0224	10	0.72032	D	0.01	.	11.4794	0.50316	0.9282:0.0:0.0717:0.0	.	767	P56715	RP1_HUMAN	D	767	ENSP00000220676:N767D	ENSP00000220676:N767D	N	+	1	0	RP1	55701294	0.638000	0.27225	0.018000	0.16275	0.594000	0.36715	4.922000	0.63404	2.270000	0.75569	0.482000	0.46254	AAT	.	.	none		0.284	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
ESRRB	2103	hgsc.bcm.edu	37	14	76966275	76966275	+	Missense_Mutation	SNP	T	T	C	rs188462546	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:76966275T>C	ENST00000509242.1	+	9	1464	c.1366T>C	c.(1366-1368)Ttc>Ctc	p.F456L	ESRRB_ENST00000261532.7_3'UTR|RP11-187O7.3_ENST00000554926.1_lincRNA|ESRRB_ENST00000380887.2_Missense_Mutation_p.F456L	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	456					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		AAAATGCCCCTTCCAATCAGC	0.552													T|||	17	0.00339457	0.0008	0.0101	5008	,	,		18910	0.0		0.0089	False		,,,				2504	0.0				p.F456L		Atlas-SNP	.											.	ESRRB	114	.	0			c.T1366C						PASS	.	T	LEU/PHE	6,4400	8.1+/-20.4	0,6,2197	86.0	74.0	78.0		1366	-1.1	0.0	14		78	42,8558	22.2+/-67.0	0,42,4258	yes	missense	ESRRB	NM_004452.3	22	0,48,6455	CC,CT,TT		0.4884,0.1362,0.3691	benign	456/509	76966275	48,12958	2203	4300	6503	SO:0001583	missense	2103	exon10			TGCCCCTTCCAAT	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"""Nuclear hormone receptors"""	3473	protein-coding gene	gene with protein product		602167	"""deafness, autosomal recessive 35"""	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.1366T>C	14.37:g.76966275T>C	ENSP00000422488:p.Phe456Leu	97.0	0.0	0		91.0	50.0	0.549451	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	5.424	0.263322	0.10294	0.001362	0.004884	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000380887	D;D;D	0.92149	-2.97;-2.98;-2.98	3.02	-1.07	0.09968	.	.	.	.	.	T	0.69602	0.3129	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.60915	-0.7168	9	0.11485	T	0.65	.	0.5481	0.00657	0.2112:0.1289:0.2174:0.4425	.	456	Q5F0P7	.	L	461;456;456	ENSP00000424992:F461L;ENSP00000422488:F456L;ENSP00000370270:F456L	ENSP00000370270:F456L	F	+	1	0	ESRRB	76036028	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.131000	0.10482	-0.206000	0.10203	0.528000	0.53228	TTC	T|0.994;C|0.006	0.006	strong		0.552	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1		
TIGD1	200765	hgsc.bcm.edu	37	2	233413842	233413842	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233413842T>C	ENST00000408957.3	-	1	1384	c.751A>G	c.(751-753)Act>Gct	p.T251A	EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000258416.3_5'Flank|MIR5001_ENST00000580185.1_RNA|EIF4E2_ENST00000409322.1_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000409098.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409495.1_5'Flank	NM_145702.1	NP_663748.1	Q96MW7	TIGD1_HUMAN	tigger transposable element derived 1	251	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|skin(1)	2		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00842)|GBM - Glioblastoma multiforme(43;0.233)		gtagatttagtataattctta	0.413																																					p.T251A		Atlas-SNP	.											.	TIGD1	17	.	0			c.A751G						PASS	.						20.0	23.0	22.0					2																	233413842		1327	2309	3636	SO:0001583	missense	200765	exon1			ATTTAGTATAATT		CCDS2495.1	2q37.1	2011-01-17			ENSG00000221944	ENSG00000221944			14523	protein-coding gene	gene with protein product		612972					Standard	NM_145702		Approved	EEYORE	uc002vsy.2	Q96MW7	OTTHUMG00000133260	ENST00000408957.3:c.751A>G	2.37:g.233413842T>C	ENSP00000386186:p.Thr251Ala	17.0	0.0	0		20.0	9.0	0.45	NM_145702	Q6P4D2|Q6PIF9	Missense_Mutation	SNP	ENST00000408957.3	37	CCDS2495.1	.	.	.	.	.	.	.	.	.	.	T	9.929	1.214229	0.22289	.	.	ENSG00000221944	ENST00000408957	T	0.41065	1.01	0.516	-0.829	0.10796	.	.	.	.	.	T	0.12603	0.0306	N	0.01048	-1.04	0.21579	N	0.99964	B	0.02656	0.0	B	0.01281	0.0	T	0.22521	-1.0214	8	0.28530	T	0.3	.	.	.	.	.	251	Q96MW7	TIGD1_HUMAN	A	251	ENSP00000386186:T251A	ENSP00000386186:T251A	T	-	1	0	TIGD1	233122086	0.968000	0.33430	0.935000	0.37517	0.927000	0.56198	-0.389000	0.07342	-0.378000	0.07918	-0.394000	0.06481	ACT	.	.	none		0.413	TIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257037.1	NM_145702	
ALAD	210	hgsc.bcm.edu	37	9	116152915	116152915	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116152915G>A	ENST00000409155.3	-	6	635	c.439C>T	c.(439-441)Cgc>Tgc	p.R147C	ALAD_ENST00000277315.5_Missense_Mutation_p.R130C|ALAD_ENST00000482001.1_5'Flank	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	147					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	AGCCGCTGGCGGCTCTCCTCA	0.632																																					p.R147C		Atlas-SNP	.											.	ALAD	36	.	0			c.C439T						PASS	.						31.0	33.0	32.0					9																	116152915		2203	4300	6503	SO:0001583	missense	210	exon6			GCTGGCGGCTCTC	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"""porphobilinogen synthase"""	125270	"""aminolevulinate, delta-, dehydratase"""			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.439C>T	9.37:g.116152915G>A	ENSP00000386284:p.Arg147Cys	40.0	0.0	0		29.0	16.0	0.551724	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	37	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933839	0.34096	.	.	ENSG00000148218	ENST00000409155;ENST00000277315	D;D	0.86865	-2.18;-2.18	5.8	3.72	0.42706	Aldolase-type TIM barrel (1);	0.131674	0.64402	N	0.000001	T	0.63438	0.2511	N	0.01277	-0.915	0.47476	D	0.999439	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.09377	0.001;0.003;0.004	T	0.59490	-0.7445	10	0.56958	D	0.05	-6.8616	3.4528	0.07505	0.2886:0.0:0.487:0.2244	.	147;130;176	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	C	147;130	ENSP00000386284:R147C;ENSP00000277315:R130C	ENSP00000277315:R130C	R	-	1	0	ALAD	115192736	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	4.589000	0.61006	1.358000	0.45922	-0.345000	0.07892	CGC	.	.	none		0.632	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	
COL1A1	1277	hgsc.bcm.edu	37	17	48269167	48269167	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48269167G>A	ENST00000225964.5	-	31	2227	c.2109C>T	c.(2107-2109)ccC>ccT	p.P703P		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	703	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	CATCGTTGCCGGGAGCACCGT	0.677			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta																														p.P703P		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	COL1A1,NS,carcinoma,-2,2	COL1A1	158	2	0			c.C2109T						scavenged	.						30.0	31.0	31.0					17																	48269167		2202	4298	6500	SO:0001819	synonymous_variant	1277	exon31			GTTGCCGGGAGCA	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.2109C>T	17.37:g.48269167G>A		29.0	0.0	0		38.0	3.0	0.0789474	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			.	.	none		0.677	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102482399	102482399	+	Silent	SNP	C	C	T	rs17541158	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102482399C>T	ENST00000360184.4	+	36	7613	c.7449C>T	c.(7447-7449)atC>atT	p.I2483I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2483					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						CCATGCAGATCGAGCAGCTGG	0.622													C|||	76	0.0151757	0.003	0.0231	5008	,	,		20649	0.0		0.0437	False		,,,				2504	0.0123				p.I2483I		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C7449T						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	49.0	37.0	41.0		7449	-4.8	0.2	14	dbSNP_123	41	405,8195	125.6+/-184.2	8,389,3903	no	coding-synonymous	DYNC1H1	NM_001376.4		8,422,6073	TT,TC,CC		4.7093,0.749,3.3677		2483/4647	102482399	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon36			GCAGATCGAGCAG	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.7449C>T	14.37:g.102482399C>T		36.0	0.0	0		47.0	23.0	0.489362	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			C|0.972;T|0.028	0.028	strong		0.622	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
GNB2	2783	hgsc.bcm.edu	37	7	100273936	100273936	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100273936C>T	ENST00000303210.4	+	2	530	c.48C>T	c.(46-48)aaC>aaT	p.N16N	GNB2_ENST00000436220.1_Intron|GNB2_ENST00000424361.1_Intron|GNB2_ENST00000393924.1_Silent_p.N16N|GNB2_ENST00000427895.1_Intron|GNB2_ENST00000393926.1_Silent_p.N16N|GNB2_ENST00000419828.1_Intron	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	16					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				AGCTCCGGAACCAGATCCGGG	0.726																																					p.N16N		Atlas-SNP	.											.	GNB2	29	.	0			c.C48T						PASS	.						20.0	19.0	19.0					7																	100273936		2185	4291	6476	SO:0001819	synonymous_variant	2783	exon2			CCGGAACCAGATC	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"""WD repeat domain containing"""	4398	protein-coding gene	gene with protein product	"""G protein, beta-2 subunit"", ""guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2"", ""signal-transducing guanine nucleotide-binding regulatory protein beta subunit"", ""transducin beta chain 2"""	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.48C>T	7.37:g.100273936C>T		109.0	0.0	0		98.0	10.0	0.102041	NM_005273	B3KPU1|P11016|P54312	Silent	SNP	ENST00000303210.4	37	CCDS5703.1																																																																																			.	.	none		0.726	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273	
FAM65B	9750	hgsc.bcm.edu	37	6	24843183	24843183	+	Silent	SNP	A	A	G	rs145837095	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24843183A>G	ENST00000259698.4	-	14	2002	c.1827T>C	c.(1825-1827)aaT>aaC	p.N609N	AL512428.1_ENST00000583229.1_RNA|FAM65B_ENST00000510784.2_Silent_p.N593N|FAM65B_ENST00000540914.1_Silent_p.N559N|FAM65B_ENST00000538035.1_Silent_p.N588N|FAM65B_ENST00000378023.4_Silent_p.N559N|FAM65B_ENST00000473070.1_5'UTR	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	609					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GTAAAAGCCCATTAAAAGCAT	0.413													A|||	8	0.00159744	0.0	0.0058	5008	,	,		18595	0.001		0.003	False		,,,				2504	0.0				p.N609N		Atlas-SNP	.											FAM65B_ENST00000259698,NS,carcinoma,-1,2	FAM65B	134	2	0			c.T1827C						PASS	.	A	,	2,3798		0,2,1898	115.0	115.0	115.0		1827,1677	-11.3	0.0	6	dbSNP_134	115	47,8187		0,47,4070	yes	coding-synonymous,coding-synonymous	FAM65B	NM_014722.2,NM_015864.2	,	0,49,5968	GG,GA,AA		0.5708,0.0526,0.4072	,	609/1069,559/592	24843183	49,11985	1900	4117	6017	SO:0001819	synonymous_variant	9750	exon14			AAGCCCATTAAAA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1827T>C	6.37:g.24843183A>G		72.0	0.0	0		87.0	68.0	0.781609	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Silent	SNP	ENST00000259698.4	37	CCDS47383.1																																																																																			A|0.998;G|0.002	0.002	strong		0.413	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
GEMIN2	8487	hgsc.bcm.edu	37	14	39587220	39587220	+	Silent	SNP	C	C	A	rs150986614	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39587220C>A	ENST00000308317.6	+	3	356	c.273C>A	c.(271-273)ccC>ccA	p.P91P	GEMIN2_ENST00000250379.8_Silent_p.P91P|GEMIN2_ENST00000396249.2_Silent_p.P91P	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	91					gene expression (GO:0010467)|mRNA processing (GO:0006397)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)											GATGCCAACCCGCCCCTGAAG	0.403													C|||	9	0.00179712	0.0	0.0086	5008	,	,		13289	0.0		0.003	False		,,,				2504	0.0				p.P91P		Atlas-SNP	.											.	.	.	.	0			c.C273A						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	58.0	55.0	56.0		273,273,273	0.9	1.0	14	dbSNP_134	56	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	GEMIN2	NM_001009182.1,NM_001009183.1,NM_003616.2	,,	0,39,6464	AA,AC,CC		0.407,0.0908,0.2999	,,	91/266,91/251,91/281	39587220	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	8487	exon3			CCAACCCGCCCCT	AF027150	CCDS9669.1, CCDS32068.1, CCDS41946.1	14q21.1	2011-08-04	2011-08-04	2011-08-04	ENSG00000092208	ENSG00000092208			10884	protein-coding gene	gene with protein product		602595	"""survival of motor neuron protein interacting protein 1"""	SIP1		9323130, 9323129, 11121410	Standard	NM_003616		Approved		uc001wuq.3	O14893	OTTHUMG00000028816	ENST00000308317.6:c.273C>A	14.37:g.39587220C>A		40.0	0.0	0		51.0	21.0	0.411765	NM_003616	B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	Silent	SNP	ENST00000308317.6	37	CCDS9669.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	9.553|9.553	1.116509|1.116509	0.20795|0.20795	9.08E-4|9.08E-4	0.00407|0.00407	ENSG00000092208|ENSG00000092208	ENST00000527381|ENST00000534684	.|.	.|.	.|.	6.12|6.12	0.916|0.916	0.19373|0.19373	.|.	0.093555|.	0.85682|.	D|.	0.000000|.	T|T	0.37785|0.37785	0.1016|0.1016	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18713|0.18713	-1.0328|-1.0328	6|4	0.48119|.	T|.	0.1|.	-14.6395|-14.6395	4.3372|4.3372	0.11092|0.11092	0.2488:0.1419:0.0:0.6094|0.2488:0.1419:0.0:0.6094	.|.	.|.	.|.	.|.	Q|S	80|86	.|.	ENSP00000434048:P80Q|.	P|R	+|+	2|1	0|0	GEMIN2|GEMIN2	38656971|38656971	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.255000|0.255000	0.18333|0.18333	0.193000|0.193000	0.20303|0.20303	-0.323000|-0.323000	0.08544|0.08544	CCG|CGC	C|0.997;A|0.003	0.003	strong		0.403	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276730.2		
LARGE	9215	hgsc.bcm.edu	37	22	34000460	34000460	+	Silent	SNP	G	G	A	rs36002910	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:34000460G>A	ENST00000354992.2	-	6	1147	c.576C>T	c.(574-576)ccC>ccT	p.P192P	LARGE_ENST00000337431.2_Silent_p.P192P|LARGE_ENST00000437602.2_Silent_p.P192P|LARGE_ENST00000397394.2_Silent_p.P192P|LARGE_ENST00000402320.1_Silent_p.P192P	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	192					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CACGCACAGCGGGCACCATCC	0.567													G|||	72	0.014377	0.0015	0.0216	5008	,	,		19700	0.0		0.0477	False		,,,				2504	0.0072				p.P192P	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.C576T						PASS	.	G	,	24,4382	30.8+/-60.4	0,24,2179	139.0	115.0	123.0		576,576	-7.5	0.9	22	dbSNP_126	123	253,8347	100.1+/-161.6	6,241,4053	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	6,265,6232	AA,AG,GG		2.9419,0.5447,2.1298	,	192/757,192/757	34000460	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	9215	exon6			CACAGCGGGCACC	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.576C>T	22.37:g.34000460G>A		86.0	0.0	0		104.0	67.0	0.644231	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			G|0.979;A|0.021	0.021	strong		0.567	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130270782G>A	ENST00000373312.3	-	11	1566	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	FAM129B_ENST00000468379.1_Intron|FAM129B_ENST00000373314.3_Silent_p.L438L	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	451					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CCTGGTGCAGGAGGGTCTCGA	0.652													G|||	118	0.0235623	0.0045	0.0389	5008	,	,		17611	0.0		0.0596	False		,,,				2504	0.0256				p.L451L		Atlas-SNP	.											.	FAM129B	84	.	0			c.C1353T						PASS	.	G	,	56,4350	55.5+/-91.7	0,56,2147	137.0	133.0	135.0		1314,1353	-1.5	1.0	9	dbSNP_120	135	570,8030	153.9+/-208.2	20,530,3750	no	coding-synonymous,coding-synonymous	FAM129B	NM_001035534.1,NM_022833.2	,	20,586,5897	AA,AG,GG		6.6279,1.271,4.8132	,	438/734,451/747	130270782	626,12380	2203	4300	6503	SO:0001819	synonymous_variant	64855	exon11			GTGCAGGAGGGTC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1353C>T	9.37:g.130270782G>A		47.0	0.0	0		41.0	17.0	0.414634	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																			G|0.957;C|0.000;A|0.043	0.043	strong		0.652	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
LMOD3	56203	hgsc.bcm.edu	37	3	69168747	69168747	+	Silent	SNP	A	A	G	rs115972674	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:69168747A>G	ENST00000420581.2	-	2	938	c.759T>C	c.(757-759)ccT>ccC	p.P253P	LMOD3_ENST00000489031.1_Silent_p.P253P|LMOD3_ENST00000475434.1_Silent_p.P253P	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	253						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		CCTTCATGTCAGGATCATTTT	0.408													A|||	63	0.0125799	0.0023	0.0231	5008	,	,		22033	0.0		0.0348	False		,,,				2504	0.0092				p.P253P		Atlas-SNP	.											.	LMOD3	92	.	0			c.T759C						PASS	.	A		21,3747		0,21,1863	182.0	167.0	172.0		759	-9.6	0.9	3	dbSNP_132	172	377,7853		10,357,3748	no	coding-synonymous	LMOD3	NM_198271.3		10,378,5611	GG,GA,AA		4.5808,0.5573,3.3172		253/561	69168747	398,11600	1884	4115	5999	SO:0001819	synonymous_variant	56203	exon2			CATGTCAGGATCA	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.759T>C	3.37:g.69168747A>G		72.0	0.0	0		57.0	31.0	0.54386	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Silent	SNP	ENST00000420581.2	37	CCDS46862.1																																																																																			A|0.979;G|0.021	0.021	strong		0.408	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
OR2T27	403239	hgsc.bcm.edu	37	1	248813470	248813470	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248813470G>A	ENST00000344889.3	-	1	715	c.716C>T	c.(715-717)gCc>gTc	p.A239V		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGAGCAGGTGGCCACAGCCTT	0.522																																					p.A239V		Atlas-SNP	.											.	OR2T27	52	.	0			c.C716T						PASS	.						48.0	32.0	38.0					1																	248813470		2184	4257	6441	SO:0001583	missense	403239	exon1			CAGGTGGCCACAG		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.716C>T	1.37:g.248813470G>A	ENSP00000342008:p.Ala239Val	84.0	0.0	0		91.0	27.0	0.296703	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	12.87	2.068166	0.36470	.	.	ENSG00000187701	ENST00000344889	T	0.00115	8.71	3.42	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.186819	0.26099	N	0.026342	T	0.00241	0.0007	L	0.34521	1.04	0.21579	N	0.999634	P	0.49696	0.927	P	0.59825	0.864	T	0.65043	-0.6264	10	0.48119	T	0.1	.	14.1834	0.65588	0.0:0.0:1.0:0.0	.	239	Q8NH04	O2T27_HUMAN	V	239	ENSP00000342008:A239V	ENSP00000342008:A239V	A	-	2	0	OR2T27	246880093	0.863000	0.29885	0.984000	0.44739	0.113000	0.19764	1.636000	0.37144	1.921000	0.55644	0.400000	0.26472	GCC	.	.	none		0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
OR4E2	26686	hgsc.bcm.edu	37	14	22133692	22133692	+	Nonsense_Mutation	SNP	C	C	A	rs553173765		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:22133692C>A	ENST00000408935.1	+	1	396	c.396C>A	c.(394-396)taC>taA	p.Y132*		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		CACTCCACTACCCCAATGTGA	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23178	0.0		0.0	False		,,,				2504	0.0				p.Y132X		Atlas-SNP	.											.	OR4E2	44	.	0			c.C396A						PASS	.						190.0	178.0	182.0					14																	22133692		2036	4208	6244	SO:0001587	stop_gained	26686	exon1			CCACTACCCCAAT		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.396C>A	14.37:g.22133692C>A	ENSP00000386195:p.Tyr132*	210.0	0.0	0		196.0	95.0	0.484694	NM_001001912	Q6IET6|Q96R62	Nonsense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532044	0.85812	.	.	ENSG00000221977	ENST00000408935	.	.	.	5.78	1.91	0.25777	.	0.000000	0.34828	U	0.003654	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3593	0.32348	0.0:0.6039:0.0:0.3961	.	.	.	.	X	132	.	ENSP00000386195:Y132X	Y	+	3	2	OR4E2	21203532	0.421000	0.25465	0.765000	0.31456	0.943000	0.58893	0.966000	0.29331	0.364000	0.24374	0.585000	0.79938	TAC	.	.	none		0.488	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
CCDC85A	114800	hgsc.bcm.edu	37	2	56603044	56603044	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:56603044C>T	ENST00000407595.2	+	5	2048	c.1546C>T	c.(1546-1548)Cct>Tct	p.P516S	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	516										breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTCCCAGCAGCCTGAACCTGT	0.488																																					p.P516S		Atlas-SNP	.											.	CCDC85A	70	.	0			c.C1546T						PASS	.						85.0	85.0	85.0					2																	56603044		2041	4187	6228	SO:0001583	missense	114800	exon5			CAGCAGCCTGAAC	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.1546C>T	2.37:g.56603044C>T	ENSP00000384040:p.Pro516Ser	177.0	0.0	0		189.0	45.0	0.238095	NM_001080433		Missense_Mutation	SNP	ENST00000407595.2	37	CCDS46290.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207790	0.39003	.	.	ENSG00000055813	ENST00000407595;ENST00000407862	.	.	.	5.15	5.15	0.70609	.	0.143817	0.32093	N	0.006595	T	0.35038	0.0918	N	0.14661	0.345	0.34306	D	0.684947	B	0.21452	0.056	B	0.19666	0.026	T	0.45600	-0.9250	9	0.52906	T	0.07	-32.921	10.7187	0.46028	0.0:0.9059:0.0:0.0941	.	516	Q96PX6	CC85A_HUMAN	S	516;105	.	ENSP00000384040:P516S	P	+	1	0	CCDC85A	56456548	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.253000	0.43205	2.673000	0.90976	0.467000	0.42956	CCT	.	.	none		0.488	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1		
ECSIT	51295	hgsc.bcm.edu	37	19	11617020	11617020	+	Silent	SNP	T	T	G	rs34645543	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11617020T>G	ENST00000270517.7	-	8	1410	c.1275A>C	c.(1273-1275)cgA>cgC	p.R425R	ZNF653_ENST00000293771.5_5'Flank|ZNF653_ENST00000593191.1_5'Flank|ECSIT_ENST00000588998.1_3'UTR|ECSIT_ENST00000591104.1_3'UTR|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000417981.2_Silent_p.R211R|ECSIT_ENST00000252440.7_3'UTR	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	425					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CCTGCTGCTGTCGCTGCAGGT	0.677													T|||	4	0.000798722	0.0	0.0014	5008	,	,		16330	0.0		0.003	False		,,,				2504	0.0				p.R425R		Atlas-SNP	.											.	ECSIT	32	.	0			c.A1275C						PASS	.	T	,,	3,4303		0,3,2150	52.0	53.0	53.0		,633,1275	0.6	0.9	19	dbSNP_126	53	13,8423		1,11,4206	no	utr-3,coding-synonymous,coding-synonymous	ECSIT	NM_001142464.2,NM_001142465.2,NM_016581.4	,,	1,14,6356	GG,GT,TT		0.1541,0.0697,0.1256	,,	,211/218,425/432	11617020	16,12726	2153	4218	6371	SO:0001819	synonymous_variant	51295	exon8			CTGCTGTCGCTGC	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"""Mitochondrial respiratory chain complex assembly factors"""	29548	protein-coding gene	gene with protein product	"""signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"""	608388	"""ECSIT homolog (Drosophila)"""			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.1275A>C	19.37:g.11617020T>G		32.0	0.0	0		44.0	26.0	0.590909	NM_016581	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Silent	SNP	ENST00000270517.7	37	CCDS12262.1																																																																																			T|0.999;G|0.001	0.001	strong		0.677	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
TMOD1	7111	hgsc.bcm.edu	37	9	100331188	100331188	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100331188A>T	ENST00000259365.4	+	8	952	c.739A>T	c.(739-741)Atg>Ttg	p.M247L	TMOD1_ENST00000375175.1_Missense_Mutation_p.M120L|TMOD1_ENST00000395211.2_Missense_Mutation_p.M247L	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	247					adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)				breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		CCTTGCTGAGATGCTCAAGGA	0.527																																					p.M247L		Atlas-SNP	.											.	TMOD1	29	.	0			c.A739T						PASS	.						118.0	110.0	113.0					9																	100331188		2203	4300	6503	SO:0001583	missense	7111	exon8			GCTGAGATGCTCA		CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD		1370827, 8661028	Standard	NM_003275		Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.739A>T	9.37:g.100331188A>T	ENSP00000259365:p.Met247Leu	102.0	0.0	0		97.0	50.0	0.515464	NM_001166116	B2RB77|Q5T7W3|Q9BUF1	Missense_Mutation	SNP	ENST00000259365.4	37	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.250806	0.80135	.	.	ENSG00000136842	ENST00000395211;ENST00000259365;ENST00000375175	D;D;D	0.92805	-3.11;-3.11;-3.11	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	M	0.64630	1.985	0.58432	D	0.999994	D	0.53885	0.963	P	0.56042	0.79	D	0.93032	0.6449	10	0.39692	T	0.17	-30.4856	14.4885	0.67634	1.0:0.0:0.0:0.0	.	247	P28289	TMOD1_HUMAN	L	247;247;120	ENSP00000378637:M247L;ENSP00000259365:M247L;ENSP00000364318:M120L	ENSP00000259365:M247L	M	+	1	0	TMOD1	99371009	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.109000	0.77062	2.135000	0.66039	0.460000	0.39030	ATG	.	.	none		0.527	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275	
ZNF597	146434	hgsc.bcm.edu	37	16	3486738	3486738	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3486738C>A	ENST00000301744.4	-	4	1196	c.961G>T	c.(961-963)Gac>Tac	p.D321Y		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	321					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(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						CGTTCAGAGTCCTCGTCGTGG	0.493																																					p.D321Y		Atlas-SNP	.											.	ZNF597	41	.	0			c.G961T						PASS	.						70.0	66.0	67.0					16																	3486738		2197	4300	6497	SO:0001583	missense	146434	exon4			CAGAGTCCTCGTC	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.961G>T	16.37:g.3486738C>A	ENSP00000301744:p.Asp321Tyr	43.0	0.0	0		38.0	9.0	0.236842	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.673850	0.29693	.	.	ENSG00000167981	ENST00000301744	T	0.07688	3.17	4.48	0.208	0.15221	.	0.346678	0.20965	N	0.082485	T	0.06005	0.0156	N	0.19112	0.55	0.09310	N	1	D	0.62365	0.991	P	0.47744	0.556	T	0.30268	-0.9984	10	0.87932	D	0	-3.4924	3.4929	0.07644	0.1755:0.4118:0.0:0.4127	.	321	Q96LX8	ZN597_HUMAN	Y	321	ENSP00000301744:D321Y	ENSP00000301744:D321Y	D	-	1	0	ZNF597	3426739	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	0.646000	0.24797	0.201000	0.20466	0.650000	0.86243	GAC	.	.	none		0.493	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
RP11-383M4.6	0	hgsc.bcm.edu	37	9	84547771	84547771	+	lincRNA	SNP	A	A	C	rs549661658	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84547771A>C	ENST00000585776.1	-	0	1039				RP11-383M4.2_ENST00000427387.1_lincRNA|SPATA31D4_ENST00000341875.4_RNA																							CAAACAAAAGATGTTGGAAGC	0.448																																					p.M899L		Atlas-SNP	.											.	.	.	.	0			c.A2695C						PASS	.						8.0	12.0	10.0					9																	84547771		669	1516	2185			389761	exon4			CAAAAGATGTTGG																													9.37:g.84547771A>C		119.0	0.0	0		109.0	45.0	0.412844	NM_001145197		Missense_Mutation	SNP	ENST00000585776.1	37																																																																																				.	.	none		0.448	RP11-383M4.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000453562.1		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121659234	121659234	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:121659234G>A	ENST00000393386.2	+	13	5311	c.4900G>A	c.(4900-4902)Gag>Aag	p.E1634K	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E774K	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1634					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GTTGGAATCCGAGAAGAAGGC	0.438																																					p.E1634K		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4900A						PASS	.						213.0	190.0	198.0					7																	121659234		2203	4300	6503	SO:0001583	missense	5803	exon13			GAATCCGAGAAGA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4900G>A	7.37:g.121659234G>A	ENSP00000377047:p.Glu1634Lys	172.0	0.0	0		173.0	9.0	0.0520231	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930084	0.92389	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.76968	0.84;-1.06	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	D	0.86640	0.5981	M	0.64997	1.995	0.54753	D	0.999989	D;P;D	0.89917	0.996;0.946;1.0	P;B;D	0.68765	0.714;0.31;0.96	D	0.87100	0.2178	10	0.59425	D	0.04	.	19.1031	0.93282	0.0:0.0:1.0:0.0	.	773;774;1634	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	K	1634;774	ENSP00000377047:E1634K;ENSP00000410000:E774K	ENSP00000377047:E1634K	E	+	1	0	PTPRZ1	121446470	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.670000	0.54569	2.539000	0.85634	0.585000	0.79938	GAG	.	.	none		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
WFIKKN1	117166	hgsc.bcm.edu	37	16	683547	683547	+	Silent	SNP	G	G	A	rs148648187	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:683547G>A	ENST00000319070.2	+	2	1459	c.1137G>A	c.(1135-1137)ccG>ccA	p.P379P		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	379	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CCTACAGCCCGCTGCTGCAGC	0.736													g|||	11	0.00219649	0.0	0.0043	5008	,	,		11845	0.0		0.008	False		,,,				2504	0.0				p.P379P		Atlas-SNP	.											.	WFIKKN1	30	.	0			c.G1137A						PASS	.			0,4188		0,0,2094	7.0	8.0	8.0		1137	-3.7	1.0	16	dbSNP_134	8	36,8240		0,36,4102	no	coding-synonymous	WFIKKN1	NM_053284.2		0,36,6196	AA,AG,GG		0.435,0.0,0.2888		379/549	683547	36,12428	2094	4138	6232	SO:0001819	synonymous_variant	117166	exon2			CAGCCCGCTGCTG	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30912	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20A"""	608021	"""chromosome 16 open reading frame 12"""	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.1137G>A	16.37:g.683547G>A		13.0	0.0	0		7.0	5.0	0.714286	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			G|0.994;A|0.006	0.006	strong		0.736	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
OR2J3	442186	hgsc.bcm.edu	37	6	29080267	29080267	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29080267G>A	ENST00000377169.1	+	1	600	c.600G>A	c.(598-600)ctG>ctA	p.L200L		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TCAATGAGCTGACCCTCATGA	0.463																																					p.L200L		Atlas-SNP	.											.	OR2J3	53	.	0			c.G600A						PASS	.						100.0	112.0	108.0					6																	29080267		1339	2597	3936	SO:0001819	synonymous_variant	442186	exon1			TGAGCTGACCCTC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.600G>A	6.37:g.29080267G>A		318.0	0.0	0		295.0	17.0	0.0576271	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	37	CCDS43433.1																																																																																			.	.	none		0.463	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
OR9G1	390174	hgsc.bcm.edu	37	11	56468431	56468431	+	Missense_Mutation	SNP	G	G	A	rs141836537	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:56468431G>A	ENST00000312153.1	+	1	568	c.568G>A	c.(568-570)Gag>Aag	p.E190K		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GGCCTGTGGCGAGAAGGGCGG	0.473													G|||	3	0.000599042	0.0015	0.0	5008	,	,		20715	0.0		0.001	False		,,,				2504	0.0				p.E190K		Atlas-SNP	.											.	.	.	.	0			c.G568A						PASS	.	G	LYS/GLU	0,4402		0,0,2201	114.0	116.0	116.0		568	-1.0	0.3	11	dbSNP_134	116	3,8589	3.0+/-9.4	0,3,4293	yes	missense	OR9G1	NM_001005213.1	56	0,3,6494	AA,AG,GG		0.0349,0.0,0.0231	benign	190/306	56468431	3,12991	2201	4296	6497	SO:0001583	missense	504191	exon1			TGTGGCGAGAAGG	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.568G>A	11.37:g.56468431G>A	ENSP00000309012:p.Glu190Lys	167.0	0.0	0		143.0	22.0	0.153846	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	7.676	0.687951	0.14973	0.0	3.49E-4	ENSG00000174914	ENST00000312153	T	0.00115	8.71	4.52	-1.04	0.10068	GPCR, rhodopsin-like superfamily (1);	1.803510	0.02484	N	0.088744	T	0.00144	0.0004	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37174	-0.9717	10	0.66056	D	0.02	-0.9116	6.1547	0.20330	0.4733:0.1374:0.3892:0.0	.	190	Q8NH87	OR9G1_HUMAN	K	190	ENSP00000309012:E190K	ENSP00000309012:E190K	E	+	1	0	OR9G1	56225007	0.000000	0.05858	0.269000	0.24586	0.178000	0.23041	0.239000	0.18023	-0.048000	0.13401	-0.510000	0.04470	GAG	G|1.000;A|0.000	0.000	weak		0.473	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
GPRC5C	55890	hgsc.bcm.edu	37	17	72436078	72436078	+	Missense_Mutation	SNP	G	G	A	rs148895616	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72436078G>A	ENST00000481232.1	+	2	809	c.298G>A	c.(298-300)Gcc>Acc	p.A100T	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Missense_Mutation_p.A67T|GPRC5C_ENST00000392627.1_Missense_Mutation_p.A100T			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	55					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						CGTCCTGGAGGCCGTGGCTGG	0.657																																					p.A100T		Atlas-SNP	.											.	GPRC5C	92	.	0			c.G298A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	59.0	57.0	58.0		199,298	5.6	1.0	17	dbSNP_134	58	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	GPRC5C	NM_018653.3,NM_022036.2	58,58	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	possibly-damaging,possibly-damaging	67/454,100/487	72436078	13,12993	2203	4300	6503	SO:0001583	missense	55890	exon2			CTGGAGGCCGTGG	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000481232.1:c.298G>A	17.37:g.72436078G>A	ENSP00000462147:p.Ala100Thr	40.0	0.0	0		29.0	15.0	0.517241	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000481232.1	37		.	.	.	.	.	.	.	.	.	.	G	9.841	1.191113	0.21954	0.0	0.001512	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000392629;ENST00000392628	T	0.22134	1.97	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.46670	1.46	0.58432	D	0.999995	P;P;P;D	0.52996	0.714;0.714;0.812;0.957	B;B;B;P	0.52758	0.194;0.194;0.355;0.708	T	0.00628	-1.1637	10	0.28530	T	0.3	-6.6765	18.5	0.90877	0.0:0.0:1.0:0.0	.	55;55;67;55	A8MXZ4;Q9NQ84;Q9NQ84-2;Q9BSP0	.;GPC5C_HUMAN;.;.	T	55;100;67;55	ENSP00000376405:A67T	ENSP00000340595:A100T	A	+	1	0	GPRC5C	69947673	1.000000	0.71417	0.995000	0.50966	0.171000	0.22731	5.341000	0.65964	2.616000	0.88540	0.561000	0.74099	GCC	G|0.999;A|0.001	0.001	strong		0.657	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2		
HCFC1	3054	hgsc.bcm.edu	37	X	153227753	153227753	+	Silent	SNP	G	G	C	rs372516617		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153227753G>C	ENST00000310441.7	-	5	1683	c.717C>G	c.(715-717)acC>acG	p.T239T	HCFC1_ENST00000369984.4_Silent_p.T239T|HCFC1_ENST00000354233.3_Silent_p.T239T|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	239					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCACGTCAGGGTGTCTGCAG	0.562																																					p.T239T		Atlas-SNP	.											.	HCFC1	284	.	0			c.C717G						PASS	.	G		1,3672		0,1,0,1550,571	56.0	58.0	58.0		717	-11.2	0.1	X		58	5,6605		0,4,1,2392,1817	no	coding-synonymous	HCFC1	NM_005334.2		0,5,1,3942,2388	CC,CG,C,GG,G		0.0756,0.0272,0.0583		239/2036	153227753	6,10277	2122	4214	6336	SO:0001819	synonymous_variant	3054	exon5			CGTCAGGGTGTCT		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.717C>G	X.37:g.153227753G>C		26.0	0.0	0		48.0	10.0	0.208333	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			.	.	weak		0.562	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
TRERF1	55809	hgsc.bcm.edu	37	6	42236973	42236973	+	Missense_Mutation	SNP	C	C	T	rs61756353	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42236973C>T	ENST00000372922.4	-	5	918	c.356G>A	c.(355-357)gGc>gAc	p.G119D	TRERF1_ENST00000541110.1_Missense_Mutation_p.G119D|TRERF1_ENST00000354325.2_Missense_Mutation_p.G119D|TRERF1_ENST00000340840.2_Missense_Mutation_p.G119D|TRERF1_ENST00000372917.4_Missense_Mutation_p.G119D	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	119					cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GTATTGGTAGCCATCAGTGGG	0.572													C|||	15	0.00299521	0.0	0.0	5008	,	,		19457	0.0		0.002	False		,,,				2504	0.0133				p.G119D		Atlas-SNP	.											.	TRERF1	124	.	0			c.G356A						PASS	.	C	ASP/GLY	3,4403	6.2+/-15.9	0,3,2200	165.0	167.0	166.0		356	4.6	1.0	6	dbSNP_129	166	29,8571	20.4+/-63.3	0,29,4271	yes	missense	TRERF1	NM_033502.2	94	0,32,6471	TT,TC,CC		0.3372,0.0681,0.246	probably-damaging	119/1201	42236973	32,12974	2203	4300	6503	SO:0001583	missense	55809	exon5			TGGTAGCCATCAG	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.356G>A	6.37:g.42236973C>T	ENSP00000362013:p.Gly119Asp	59.0	0.0	0		90.0	19.0	0.211111	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.88	2.964211	0.53507	6.81E-4	0.003372	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.18960	2.43;2.18;2.37;2.18;2.19	5.5	4.61	0.57282	.	0.096885	0.45361	D	0.000363	T	0.23886	0.0578	L	0.32530	0.975	0.37383	D	0.912135	D;D;D	0.76494	0.999;0.995;0.995	D;P;P	0.71414	0.973;0.878;0.878	T	0.07908	-1.0748	10	0.87932	D	0	-9.923	14.61	0.68510	0.0:0.7229:0.2771:0.0	rs61756353	119;119;119	Q96PN7-4;Q05GC8;Q96PN7	.;.;TREF1_HUMAN	D	119	ENSP00000439689:G119D;ENSP00000362008:G119D;ENSP00000362013:G119D;ENSP00000339438:G119D;ENSP00000346285:G119D	ENSP00000339438:G119D	G	-	2	0	TRERF1	42344951	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	3.339000	0.52135	1.291000	0.44653	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.572	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130742413C>T	ENST00000373095.1	-	1	379	c.4G>A	c.(4-6)Gct>Act	p.A2T		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	2										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						ATCAAGAAAGCCATGAGCGAG	0.517																																					p.A2T		Atlas-SNP	.											.	FAM102A	32	.	0			c.G4A						PASS	.						89.0	103.0	98.0					9																	130742413		2203	4300	6503	SO:0001583	missense	399665	exon1			AGAAAGCCATGAG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.4G>A	9.37:g.130742413C>T	ENSP00000362187:p.Ala2Thr	65.0	0.0	0		66.0	15.0	0.227273	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141355	0.57044	.	.	ENSG00000167106	ENST00000373095	.	.	.	4.76	4.76	0.60689	.	0.117104	0.56097	D	0.000025	T	0.54013	0.1832	L	0.43152	1.355	0.80722	D	1	B	0.29162	0.235	B	0.17098	0.017	T	0.55023	-0.8205	9	0.42905	T	0.14	-9.6451	16.7632	0.85517	0.0:1.0:0.0:0.0	.	2	Q5T9C2	F102A_HUMAN	T	2	.	ENSP00000362187:A2T	A	-	1	0	FAM102A	129782234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.711000	0.54868	2.185000	0.69588	0.462000	0.41574	GCT	.	.	none		0.517	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
CNGB1	1258	hgsc.bcm.edu	37	16	58001086	58001086	+	Silent	SNP	C	C	T	rs61997250	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58001086C>T	ENST00000251102.8	-	2	165	c.105G>A	c.(103-105)gcG>gcA	p.A35A	CNGB1_ENST00000311183.4_Silent_p.A35A|CNGB1_ENST00000564448.1_Silent_p.A35A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	35	Glu-rich.				cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						GTTCCACCTCCGCCTCCATCT	0.647													C|||	41	0.0081869	0.0023	0.0072	5008	,	,		17304	0.0		0.0258	False		,,,				2504	0.0072				p.A35A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G105A						PASS	.	C	,	32,3990		0,32,1979	96.0	101.0	99.0		105,105	-8.9	0.0	16	dbSNP_129	99	242,8090		4,234,3928	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	4,266,5907	TT,TC,CC		2.9045,0.7956,2.2179	,	35/300,35/1252	58001086	274,12080	2011	4166	6177	SO:0001819	synonymous_variant	1258	exon2			CACCTCCGCCTCC	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.105G>A	16.37:g.58001086C>T		56.0	0.0	0		46.0	20.0	0.434783	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
S100A7	6278	hgsc.bcm.edu	37	1	153431435	153431435	+	Missense_Mutation	SNP	T	T	G	rs72708760	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153431435T>G	ENST00000368723.3	-	2	165	c.55A>C	c.(55-57)Aaa>Caa	p.K19Q	S100A7_ENST00000368722.1_Missense_Mutation_p.K19Q	NM_002963.3	NP_002954.2	P31151	S10A7_HUMAN	S100 calcium binding protein A7	19	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				angiogenesis (GO:0001525)|defense response to Gram-negative bacterium (GO:0050829)|epidermis development (GO:0008544)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of granulocyte chemotaxis (GO:0071624)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of T cell chemotaxis (GO:0010820)|response to lipopolysaccharide (GO:0032496)|response to reactive oxygen species (GO:0000302)|sequestering of metal ion (GO:0051238)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(5)|skin(2)	10	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGGTGTATTTGTGAAACATG	0.428													T|||	8	0.00159744	0.0	0.0014	5008	,	,		20640	0.0		0.007	False		,,,				2504	0.0				p.K19Q		Atlas-SNP	.											.	S100A7	23	.	0			c.A55C						PASS	.	T	GLN/LYS	4,4402		0,4,2199	271.0	231.0	244.0		55	-0.5	0.0	1	dbSNP_130	244	52,8548		0,52,4248	yes	missense	S100A7	NM_002963.3	53	0,56,6447	GG,GT,TT		0.6047,0.0908,0.4306	benign	19/102	153431435	56,12950	2203	4300	6503	SO:0001583	missense	6278	exon2			TGTATTTGTGAAA	BC034687	CCDS1039.1	1q21	2013-01-10	2006-09-11		ENSG00000143556	ENSG00000143556		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10497	protein-coding gene	gene with protein product		600353	"""S100 calcium-binding protein A7 (psoriasin 1)"", ""S100 calcium binding protein A7 (psoriasin 1)"""	PSOR1		1940442	Standard	NM_002963		Approved	S100A7c	uc001fbv.1	P31151	OTTHUMG00000013123	ENST00000368723.3:c.55A>C	1.37:g.153431435T>G	ENSP00000357712:p.Lys19Gln	177.0	0.0	0		160.0	77.0	0.48125	NM_002963	Q5SY67|Q6FGE3|Q9H1E2	Missense_Mutation	SNP	ENST00000368723.3	37	CCDS1039.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	6.578	0.475062	0.12521	9.08E-4	0.006047	ENSG00000143556	ENST00000368723;ENST00000368722	T;T	0.08896	3.04;3.04	2.1	-0.492	0.12041	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01222	0.0040	L	0.33485	1.01	0.09310	N	1	B	0.22683	0.073	B	0.24394	0.053	T	0.48234	-0.9053	9	0.08381	T	0.77	.	2.3716	0.04331	0.0:0.2008:0.3031:0.4961	.	19	P31151	S10A7_HUMAN	Q	19	ENSP00000357712:K19Q;ENSP00000357711:K19Q	ENSP00000357711:K19Q	K	-	1	0	S100A7	151698059	0.004000	0.15560	0.001000	0.08648	0.747000	0.42532	0.196000	0.17176	-0.097000	0.12307	0.163000	0.16589	AAA	T|0.997;G|0.003	0.003	strong		0.428	S100A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036789.1	NM_002963	
C1orf101	257044	hgsc.bcm.edu	37	1	244715882	244715882	+	Silent	SNP	A	A	G	rs34510134	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:244715882A>G	ENST00000366534.4	+	9	849	c.795A>G	c.(793-795)tcA>tcG	p.S265S	C1orf101_ENST00000366533.4_Silent_p.S265S|C1orf101_ENST00000366531.3_Silent_p.S114S|C1orf101_ENST00000473875.1_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	265						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			CAACTGATTCATTCAAATCTT	0.458													A|||	307	0.0613019	0.2231	0.0159	5008	,	,		15160	0.0		0.001	False		,,,				2504	0.0				p.S265S		Atlas-SNP	.											.	C1orf101	158	.	0			c.A795G						PASS	.	A	,,	846,3560	334.9+/-303.7	85,676,1442	149.0	135.0	140.0		795,342,795	-0.5	1.0	1	dbSNP_126	140	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	85,686,5732	GG,GA,AA		0.1163,19.2011,6.5816	,,	265/952,114/801,265/833	244715882	856,12150	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon9			TGATTCATTCAAA	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.795A>G	1.37:g.244715882A>G		227.0	0.0	0		194.0	86.0	0.443299	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			A|0.933;G|0.067	0.067	strong		0.458	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
NEK5	341676	hgsc.bcm.edu	37	13	52661569	52661569	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:52661569C>T	ENST00000355568.4	-	15	1436	c.1297G>A	c.(1297-1299)Gag>Aag	p.E433K		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	433					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		TAATTTGGCTCGGCAGAAGAT	0.368																																					p.E433K		Atlas-SNP	.											.	NEK5	189	.	0			c.G1297A						PASS	.						130.0	121.0	124.0					13																	52661569		2203	4300	6503	SO:0001583	missense	341676	exon15			TTGGCTCGGCAGA	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1297G>A	13.37:g.52661569C>T	ENSP00000347767:p.Glu433Lys	82.0	0.0	0		126.0	65.0	0.515873	NM_199289	Q5TAP5	Missense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833151	0.71258	.	.	ENSG00000197168	ENST00000355568	T	0.74421	-0.84	5.45	5.45	0.79879	.	0.090427	0.47455	D	0.000234	T	0.78355	0.4270	L	0.59436	1.845	0.29341	N	0.866027	D	0.71674	0.998	P	0.52793	0.709	T	0.75560	-0.3275	10	0.41790	T	0.15	.	14.7893	0.69827	0.0:1.0:0.0:0.0	.	433	Q6P3R8	NEK5_HUMAN	K	433	ENSP00000347767:E433K	ENSP00000347767:E433K	E	-	1	0	NEK5	51559570	1.000000	0.71417	0.798000	0.32154	0.440000	0.31957	3.947000	0.56652	2.548000	0.85928	0.655000	0.94253	GAG	.	.	none		0.368	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
SFSWAP	6433	hgsc.bcm.edu	37	12	132239988	132239988	+	Silent	SNP	G	G	A	rs139034136	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132239988G>A	ENST00000261674.4	+	10	1653	c.1512G>A	c.(1510-1512)caG>caA	p.Q504Q	SFSWAP_ENST00000541286.1_Silent_p.Q504Q|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	504					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						TTAAGAAGCAGTTCTTCCTCC	0.468											OREG0022261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0014	5008	,	,		20727	0.0		0.001	False		,,,				2504	0.0				p.Q504Q		Atlas-SNP	.											.	SFSWAP	69	.	0			c.G1512A						PASS	.	G		0,4406	2.1+/-5.4	0,0,2203	94.0	93.0	93.0		1512	2.7	1.0	12	dbSNP_134	93	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous	SFSWAP	NM_004592.2		0,18,6485	AA,AG,GG		0.2093,0.0,0.1384		504/952	132239988	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon10			GAAGCAGTTCTTC	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1512G>A	12.37:g.132239988G>A		33.0	0.0	0	1593	28.0	10.0	0.357143	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	9.086	1.000626	0.19121	0.0	0.002093	ENSG00000061936	ENST00000537164	.	.	.	5.49	2.69	0.31865	.	.	.	.	.	T	0.53834	0.1821	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42649	-0.9439	4	.	.	.	-28.6537	5.5838	0.17264	0.2878:0.1317:0.5806:0.0	.	.	.	.	N	144	.	.	S	+	2	0	SFSWAP	130805941	0.979000	0.34478	1.000000	0.80357	0.983000	0.72400	0.103000	0.15292	0.289000	0.22422	0.561000	0.74099	AGT	G|0.999;A|0.001	0.001	strong		0.468	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
CARF	79800	hgsc.bcm.edu	37	2	203847044	203847044	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:203847044G>A	ENST00000402905.3	+	15	2260	c.1939G>A	c.(1939-1941)Gag>Aag	p.E647K	CARF_ENST00000320443.8_Missense_Mutation_p.E647K|CARF_ENST00000414439.1_Missense_Mutation_p.E545K|CARF_ENST00000438828.2_Missense_Mutation_p.E647K|CARF_ENST00000545253.1_Missense_Mutation_p.E559K|WDR12_ENST00000477723.1_Intron|CARF_ENST00000545262.1_Missense_Mutation_p.E571K|CARF_ENST00000428585.1_Missense_Mutation_p.E571K	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	647					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCAATGGACGAGCTGGTAGA	0.428																																					p.E647K		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.G1939A						PASS	.						89.0	85.0	86.0					2																	203847044		1918	4142	6060	SO:0001583	missense	79800	exon16			ATGGACGAGCTGG	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"""calcium-response factor"""	607586	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"""	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1939G>A	2.37:g.203847044G>A	ENSP00000384006:p.Glu647Lys	139.0	0.0	0		170.0	52.0	0.305882	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431639	0.62844	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.83	4.96	0.65561	.	0.075586	0.53938	D	0.000052	T	0.26521	0.0648	N	0.08118	0	0.25176	N	0.990241	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.10450	0.005;0.005;0.005	T	0.26467	-1.0102	9	0.66056	D	0.02	-2.4529	14.485	0.67611	0.0:0.8521:0.1479:0.0	.	559;571;647	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	K	647;545;571;559;571;647;647	.	ENSP00000316224:E647K	E	+	1	0	ALS2CR8	203555289	1.000000	0.71417	0.999000	0.59377	0.741000	0.42261	3.706000	0.54830	1.487000	0.48415	-0.133000	0.14855	GAG	.	.	none		0.428	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586	
ENPP2	5168	hgsc.bcm.edu	37	8	120569870	120569870	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:120569870C>T	ENST00000075322.6	-	25	2541	c.2483G>A	c.(2482-2484)cGt>cAt	p.R828H	ENPP2_ENST00000427067.2_Missense_Mutation_p.R849H|ENPP2_ENST00000259486.6_Missense_Mutation_p.R880H|ENPP2_ENST00000522167.1_Missense_Mutation_p.R463H|ENPP2_ENST00000522826.1_Missense_Mutation_p.R853H	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	828					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTCAATGTCACGCACCCTAGC	0.458																																					p.R880H	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.G2639A						PASS	.						240.0	213.0	222.0					8																	120569870		2203	4300	6503	SO:0001583	missense	5168	exon26			ATGTCACGCACCC	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2483G>A	8.37:g.120569870C>T	ENSP00000075322:p.Arg828His	108.0	0.0	0		106.0	5.0	0.0471698	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737032	0.89482	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.91	5.91	0.95273	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.051359	0.85682	D	0.000000	T	0.60818	0.2298	M	0.78637	2.42	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	T	0.62105	-0.6924	10	0.87932	D	0	.	20.3053	0.98627	0.0:1.0:0.0:0.0	.	366;853;828;880;463	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	H	880;849;463;853;828	ENSP00000259486:R880H;ENSP00000403315:R849H;ENSP00000429476:R463H;ENSP00000428291:R853H;ENSP00000075322:R828H	ENSP00000075322:R828H	R	-	2	0	ENPP2	120639051	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.989000	0.70587	2.808000	0.96608	0.655000	0.94253	CGT	.	.	none		0.458	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
ZNF652	22834	hgsc.bcm.edu	37	17	47394825	47394825	+	Missense_Mutation	SNP	G	G	C	rs181916483	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:47394825G>C	ENST00000362063.2	-	2	581	c.263C>G	c.(262-264)tCt>tGt	p.S88C	ZNF652_ENST00000430262.2_Missense_Mutation_p.S88C	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	88	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			ATGCACGTCAGACACTGCTCT	0.463													G|||	3	0.000599042	0.0	0.0014	5008	,	,		22639	0.0		0.002	False		,,,				2504	0.0				p.S88C		Atlas-SNP	.											ZNF652,NS,haematopoietic_neoplasm,0,3	ZNF652	54	3	0			c.C263G						PASS	.	G	CYS/SER,CYS/SER	1,4405	4.2+/-10.8	0,1,2202	179.0	142.0	155.0		263,263	5.7	1.0	17		155	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	ZNF652	NM_001145365.1,NM_014897.2	112,112	0,13,6490	CC,CG,GG		0.1395,0.0227,0.1	possibly-damaging,possibly-damaging	88/607,88/607	47394825	13,12993	2203	4300	6503	SO:0001583	missense	22834	exon2			ACGTCAGACACTG	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"""Zinc fingers, C2H2-type"""	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.263C>G	17.37:g.47394825G>C	ENSP00000354686:p.Ser88Cys	226.0	1.0	0.00442478		211.0	108.0	0.511848	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	9.061	0.994478	0.19043	2.27E-4	0.001395	ENSG00000198740	ENST00000362063;ENST00000430262	D;D	0.98958	-5.27;-5.27	5.74	5.74	0.90152	.	0.448368	0.27371	N	0.019676	D	0.94663	0.8279	N	0.14661	0.345	0.26476	N	0.975184	P	0.34462	0.454	B	0.29524	0.103	D	0.90267	0.4305	10	0.56958	D	0.05	-5.273	10.1922	0.43032	0.0:0.1844:0.6819:0.1337	.	88	Q9Y2D9	ZN652_HUMAN	C	88	ENSP00000354686:S88C;ENSP00000416305:S88C	ENSP00000354686:S88C	S	-	2	0	ZNF652	44749824	0.998000	0.40836	0.974000	0.42286	0.980000	0.70556	2.293000	0.43558	2.715000	0.92844	0.655000	0.94253	TCT	G|0.998;C|0.002	0.002	strong		0.463	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897	
INTS6	26512	hgsc.bcm.edu	37	13	51950198	51950198	+	Missense_Mutation	SNP	T	T	C	rs144918317	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:51950198T>C	ENST00000311234.4	-	13	2187	c.1715A>G	c.(1714-1716)aAa>aGa	p.K572R	INTS6_ENST00000490542.1_Missense_Mutation_p.K256R|INTS6_ENST00000425000.1_Missense_Mutation_p.K140R|INTS6_ENST00000463928.1_Intron|INTS6_ENST00000497989.1_Missense_Mutation_p.K394R|INTS6_ENST00000398119.2_Missense_Mutation_p.K559R	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	572					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		GTCCTGTCCTTTCAGAAATCT	0.323													T|||	3	0.000599042	0.0	0.0	5008	,	,		16958	0.0		0.003	False		,,,				2504	0.0				p.K572R		Atlas-SNP	.											.	INTS6	72	.	0			c.A1715G						PASS	.	T	ARG/LYS,ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	89.0	87.0	87.0		1676,1715	5.5	1.0	13	dbSNP_134	87	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense	INTS6	NM_001039937.1,NM_012141.2	26,26	0,13,6490	CC,CT,TT		0.1395,0.0227,0.1	benign,benign	559/875,572/888	51950198	13,12993	2203	4300	6503	SO:0001583	missense	26512	exon13			TGTCCTTTCAGAA	AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"""DEAD-boxes"""	14879	protein-coding gene	gene with protein product		604331	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"""	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.1715A>G	13.37:g.51950198T>C	ENSP00000310260:p.Lys572Arg	67.0	0.0	0		87.0	26.0	0.298851	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	37	CCDS9428.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.746	1.166106	0.21621	2.27E-4	0.001395	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989;ENST00000425000;ENST00000490542	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.48	5.48	0.80851	.	0.049655	0.85682	D	0.000000	T	0.19485	0.0468	N	0.16233	0.39	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.07908	-1.0748	10	0.13853	T	0.58	-20.7448	14.7523	0.69536	0.0:0.0:0.0:1.0	.	572	Q9UL03	INT6_HUMAN	R	572;559;394;140;256	ENSP00000310260:K572R;ENSP00000381187:K559R;ENSP00000419871:K394R;ENSP00000406915:K140R;ENSP00000419984:K256R	ENSP00000310260:K572R	K	-	2	0	INTS6	50848199	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.248000	0.58760	2.085000	0.62840	0.528000	0.53228	AAA	T|0.999;C|0.001	0.001	strong		0.323	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141	
ABCA7	10347	hgsc.bcm.edu	37	19	1056183	1056183	+	Missense_Mutation	SNP	C	C	T	rs144562001	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1056183C>T	ENST00000263094.6	+	32	4588	c.4357C>T	c.(4357-4359)Cgt>Tgt	p.R1453C	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1453C|ABCA7_ENST00000435683.2_Missense_Mutation_p.R1315C	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1453					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCCTCGACCGTGTCCTGAA	0.677																																					p.R1453C		Atlas-SNP	.											.	ABCA7	174	.	0			c.C4357T						PASS	.	C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	46.0	50.0	49.0		4357	3.3	0.0	19	dbSNP_134	49	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ABCA7	NM_019112.3	180	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	probably-damaging	1453/2147	1056183	8,12998	2203	4300	6503	SO:0001583	missense	10347	exon32			CTCGACCGTGTCC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.4357C>T	19.37:g.1056183C>T	ENSP00000263094:p.Arg1453Cys	36.0	0.0	0		39.0	20.0	0.512821	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878421	0.51801	4.54E-4	6.98E-4	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87334	-2.24;-2.24	3.28	3.28	0.37604	.	.	.	.	.	D	0.91744	0.7389	M	0.80028	2.48	0.24069	N	0.995988	D	0.62365	0.991	P	0.58970	0.849	D	0.83846	0.0260	9	0.87932	D	0	.	11.7386	0.51780	0.0:1.0:0.0:0.0	.	1453	Q8IZY2	ABCA7_HUMAN	C	1453	ENSP00000263094:R1453C;ENSP00000414062:R1453C	ENSP00000263094:R1453C	R	+	1	0	ABCA7	1007183	0.004000	0.15560	0.040000	0.18447	0.052000	0.14988	1.048000	0.30379	1.859000	0.53934	0.561000	0.74099	CGT	C|0.999;G|0.000;T|0.000	0.000	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
RIN2	54453	hgsc.bcm.edu	37	20	19955473	19955473	+	Silent	SNP	C	C	T	rs41306763	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:19955473C>T	ENST00000255006.6	+	8	1100	c.951C>T	c.(949-951)gcC>gcT	p.A317A	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	268					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CCAACGGGGCCCTGTGCTTTA	0.557													C|||	23	0.00459265	0.0008	0.0072	5008	,	,		13957	0.0		0.0169	False		,,,				2504	0.0				p.A317A		Atlas-SNP	.											.	RIN2	126	.	0			c.C951T						PASS	.	C	,	12,3852		0,12,1920	66.0	71.0	70.0		951,804	3.5	1.0	20	dbSNP_127	70	188,8048		2,184,3932	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	2,196,5852	TT,TC,CC		2.2827,0.3106,1.6529	,	317/945,268/896	19955473	200,11900	1932	4118	6050	SO:0001819	synonymous_variant	54453	exon8			CGGGGCCCTGTGC	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.951C>T	20.37:g.19955473C>T		61.0	0.0	0		105.0	53.0	0.504762	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
GALNT8	26290	hgsc.bcm.edu	37	12	4835923	4835923	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4835923A>C	ENST00000252318.2	+	2	774	c.437A>C	c.(436-438)aAg>aCg	p.K146T	RP11-234B24.6_ENST00000544741.2_3'UTR	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	146					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						CTCTTCCGGAAGTTTGGTTAC	0.557																																					p.K146T	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.A437C						PASS	.						76.0	70.0	72.0					12																	4835923		2203	4300	6503	SO:0001583	missense	26290	exon2			TCCGGAAGTTTGG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.437A>C	12.37:g.4835923A>C	ENSP00000252318:p.Lys146Thr	53.0	0.0	0		52.0	14.0	0.269231	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	A	9.701	1.154514	0.21371	.	.	ENSG00000130035	ENST00000252318	T	0.55413	0.52	4.02	-0.0796	0.13710	.	0.506417	0.15357	N	0.266621	T	0.38161	0.1030	L	0.59436	1.845	0.09310	N	0.999995	P	0.35656	0.514	B	0.30646	0.118	T	0.25847	-1.0120	10	0.46703	T	0.11	.	2.4773	0.04579	0.533:0.0:0.2436:0.2233	.	146	Q9NY28	GALT8_HUMAN	T	146	ENSP00000252318:K146T	ENSP00000252318:K146T	K	+	2	0	GALNT8	4706184	0.066000	0.20996	0.379000	0.26080	0.923000	0.55619	0.165000	0.16564	0.148000	0.19059	-0.274000	0.10170	AAG	.	.	none		0.557	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
SCAF11	9169	hgsc.bcm.edu	37	12	46320944	46320944	+	Missense_Mutation	SNP	C	C	T	rs28930670	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:46320944C>T	ENST00000369367.3	-	11	2773	c.2540G>A	c.(2539-2541)cGt>cAt	p.R847H	SCAF11_ENST00000549162.1_Missense_Mutation_p.R655H|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.R847H|SCAF11_ENST00000465950.1_Missense_Mutation_p.R532H	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	847	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GGACTGAGAACGGGATTTTTT	0.468													C|||	38	0.00758786	0.0	0.0159	5008	,	,		16776	0.0		0.0249	False		,,,				2504	0.002				p.R847H		Atlas-SNP	.											.	SCAF11	145	.	0			c.G2540A						PASS	.	C	HIS/ARG	31,4375	36.8+/-68.6	0,31,2172	122.0	121.0	122.0		2540	5.0	1.0	12	dbSNP_125	122	316,8284	113.1+/-173.2	8,300,3992	yes	missense	SCAF11	NM_004719.2	29	8,331,6164	TT,TC,CC		3.6744,0.7036,2.668	benign	847/1464	46320944	347,12659	2203	4300	6503	SO:0001583	missense	9169	exon11			TGAGAACGGGATT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2540G>A	12.37:g.46320944C>T	ENSP00000358374:p.Arg847His	155.0	0.0	0		147.0	72.0	0.489796	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	25	0.011446886446886446	0	0.0	9	0.024861878453038673	0	0.0	16	0.021108179419525065	C	13.16	2.153957	0.38021	0.007036	0.036744	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49720	1.41;2.13;1.41;2.13;0.77	5.93	5.04	0.67666	.	0.190692	0.36374	N	0.002635	T	0.10208	0.0250	L	0.48362	1.52	0.25928	N	0.983024	P;B	0.41947	0.766;0.14	B;B	0.33121	0.158;0.015	T	0.17837	-1.0356	10	0.48119	T	0.1	-9.1648	8.541	0.33393	0.2631:0.6671:0.0:0.0698	rs28930670	655;847	F8VXG7;Q99590	.;SCAFB_HUMAN	H	532;847;655;847;787	ENSP00000449812:R532H;ENSP00000358374:R847H;ENSP00000448864:R655H;ENSP00000413036:R847H;ENSP00000446746:R787H	ENSP00000358374:R847H	R	-	2	0	SCAF11	44607211	0.379000	0.25123	0.997000	0.53966	0.912000	0.54170	0.485000	0.22324	1.518000	0.48934	0.655000	0.94253	CGT	C|0.978;T|0.022	0.022	strong		0.468	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
SLC9A8	23315	hgsc.bcm.edu	37	20	48503306	48503306	+	Silent	SNP	G	G	A	rs73125686	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:48503306G>A	ENST00000361573.2	+	15	1551	c.1509G>A	c.(1507-1509)tcG>tcA	p.S503S	SLC9A8_ENST00000541138.1_Silent_p.S203S|SLC9A8_ENST00000490250.1_3'UTR|SLC9A8_ENST00000417961.1_Silent_p.S519S|SLC9A8_ENST00000539601.1_Silent_p.S284S			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	503					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			CTGTGGAGTCGGAGCACCTGT	0.662													G|||	7	0.00139776	0.0	0.0	5008	,	,		18613	0.0		0.007	False		,,,				2504	0.0				p.S519S		Atlas-SNP	.											.	SLC9A8	63	.	0			c.G1557A						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	107.0	86.0	93.0		1509	-5.8	1.0	20	dbSNP_130	93	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous	SLC9A8	NM_015266.1		0,67,6436	AA,AG,GG		0.6163,0.3177,0.5151		503/582	48503306	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon15			GGAGTCGGAGCAC	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"""Solute carriers"""	20728	protein-coding gene	gene with protein product		612730	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 8"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 8"""			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.1509G>A	20.37:g.48503306G>A		64.0	0.0	0		105.0	55.0	0.52381	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			G|0.996;A|0.004	0.004	strong		0.662	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
MUC4	4585	hgsc.bcm.edu	37	3	195512439	195512439	+	Silent	SNP	G	G	A	rs112365404	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195512439G>A	ENST00000463781.3	-	2	6471	c.6012C>T	c.(6010-6012)acC>acT	p.T2004T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2004T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACCGGAA	0.597													.|||	377	0.0752796	0.2542	0.0245	5008	,	,		27068	0.0		0.0109	False		,,,				2504	0.0133				p.T2004T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6012T						PASS	.	G	,,	232,1098		54,124,487	39.0	41.0	40.0		,6012,		0.1	3	dbSNP_132	40	59,3109		3,53,1528	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	57,177,2015	AA,AG,GG		1.8624,17.4436,6.4695	,,	,2004/5413,	195512439	291,4207	665	1584	2249	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6012C>T	3.37:g.195512439G>A		125.0	0.0	0		148.0	34.0	0.22973	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HIRA	7290	hgsc.bcm.edu	37	22	19385570	19385570	+	Silent	SNP	T	T	C	rs373432911		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19385570T>C	ENST00000263208.5	-	6	694	c.438A>G	c.(436-438)ctA>ctG	p.L146L	HIRA_ENST00000546308.1_Silent_p.L102L|HIRA_ENST00000541063.1_Silent_p.L102L|HIRA_ENST00000464189.1_5'Flank|HIRA_ENST00000340170.4_Silent_p.L146L	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	146					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					TGCATGAGGCTAGCCAGGCAT	0.517																																					p.L146L		Atlas-SNP	.											.	HIRA	100	.	0			c.A438G						PASS	.	T		0,4406		0,0,2203	103.0	85.0	91.0		438	-3.9	1.0	22		91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HIRA	NM_003325.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		146/1018	19385570	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7290	exon6			TGAGGCTAGCCAG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.438A>G	22.37:g.19385570T>C		77.0	0.0	0		86.0	49.0	0.569767	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			.	.	weak		0.517	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
PCDH10	57575	hgsc.bcm.edu	37	4	134072185	134072185	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:134072185C>T	ENST00000264360.5	+	1	1716	c.890C>T	c.(889-891)gCg>gTg	p.A297V	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	297	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		TCGCCCCGGGCGCGGGAGCTT	0.632																																					p.A297V		Atlas-SNP	.											.	PCDH10	290	.	0			c.C890T						PASS	.						41.0	45.0	43.0					4																	134072185		2203	4300	6503	SO:0001583	missense	57575	exon1			CCCGGGCGCGGGA	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"""Cadherins / Protocadherins : Non-clustered"""	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.890C>T	4.37:g.134072185C>T	ENSP00000264360:p.Ala297Val	48.0	0.0	0		39.0	9.0	0.230769	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.492356	0.01009	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.37058	1.22	4.33	3.47	0.39725	Cadherin (4);Cadherin-like (1);	0.000000	0.44902	D	0.000402	T	0.11537	0.0281	N	0.02658	-0.545	0.36301	D	0.857014	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.002	T	0.24404	-1.0161	10	0.02654	T	1	.	7.7575	0.28933	0.0:0.7463:0.166:0.0877	.	297;297	Q9P2E7;Q96SF0	PCD10_HUMAN;.	V	297	ENSP00000264360:A297V	ENSP00000264360:A297V	A	+	2	0	PCDH10	134291635	0.980000	0.34600	0.451000	0.26982	0.421000	0.31385	2.230000	0.42999	0.991000	0.38814	-0.416000	0.06073	GCG	.	.	none		0.632	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605777	84605777	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84605777G>A	ENST00000344803.2	+	4	439	c.392G>A	c.(391-393)cGg>cAg	p.R131Q		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	131					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCCGTCTGTCGGGTGTGTAAG	0.552																																					p.R131Q		Atlas-SNP	.											.	.	.	.	0			c.G392A						PASS	.						107.0	102.0	104.0					9																	84605777		1984	4157	6141	SO:0001583	missense	389763	exon4			TCTGTCGGGTGTG		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.392G>A	9.37:g.84605777G>A	ENSP00000341988:p.Arg131Gln	152.0	0.0	0		170.0	84.0	0.494118	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	g	8.742	0.919112	0.17982	.	.	ENSG00000214929	ENST00000344803	T	0.04360	3.64	2.98	0.49	0.16861	.	1.929580	0.02564	N	0.097117	T	0.02688	0.0081	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40365	-0.9567	10	0.56958	D	0.05	-1.5821	3.4169	0.07378	0.6335:0.2342:0.1323:0.0	.	131	Q6ZQQ2	F75D1_HUMAN	Q	131	ENSP00000341988:R131Q	ENSP00000341988:R131Q	R	+	2	0	FAM75D1	83795597	0.976000	0.34144	0.135000	0.22099	0.000000	0.00434	0.412000	0.21131	0.092000	0.17331	-1.291000	0.01355	CGG	.	.	none		0.552	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
CCDC178	374864	hgsc.bcm.edu	37	18	30825388	30825388	+	Missense_Mutation	SNP	G	G	A	rs146565345	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:30825388G>A	ENST00000383096.3	-	15	1596	c.1414C>T	c.(1414-1416)Cgg>Tgg	p.R472W	CCDC178_ENST00000300227.8_Missense_Mutation_p.R472W|CCDC178_ENST00000402325.1_Missense_Mutation_p.R472W|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Missense_Mutation_p.R472W|CCDC178_ENST00000583930.1_Missense_Mutation_p.R472W|CCDC178_ENST00000579947.1_Missense_Mutation_p.R472W|CCDC178_ENST00000403303.1_Missense_Mutation_p.R472W			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	472																	GATTTTTTCCGTATGCTGTAA	0.234													G|||	5	0.000998403	0.0015	0.0	5008	,	,		17240	0.001		0.002	False		,,,				2504	0.0				p.R472W		Atlas-SNP	.											C18orf34_ENST00000383096,NS,carcinoma,0,2	.	.	2	0			c.C1414T						PASS	.	G	TRP/ARG,TRP/ARG	17,4385		0,17,2184	56.0	51.0	53.0		1414,1414	2.3	0.4	18	dbSNP_134	53	7,8575		0,7,4284	yes	missense,missense	C18orf34	NM_001105528.1,NM_198995.2	101,101	0,24,6468	AA,AG,GG		0.0816,0.3862,0.1848	probably-damaging,probably-damaging	472/868,472/830	30825388	24,12960	2201	4291	6492	SO:0001583	missense	374864	exon14			TTTTCCGTATGCT	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1414C>T	18.37:g.30825388G>A	ENSP00000372576:p.Arg472Trp	52.0	0.0	0		54.0	22.0	0.407407	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0.714	-0.786183	0.02907	0.003862	8.16E-4	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36	4.75	2.33	0.28932	.	.	.	.	.	T	0.40932	0.1137	L	0.42245	1.32	0.20703	N	0.999865	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	P;P;P;P	0.56751	0.805;0.805;0.805;0.805	T	0.19128	-1.0315	9	0.87932	D	0	-0.5487	5.0078	0.14297	0.0:0.0961:0.1867:0.7172	.	472;472;472;472	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	W	472	ENSP00000385591:R472W;ENSP00000372576:R472W;ENSP00000300227:R472W;ENSP00000385867:R472W;ENSP00000385234:R472W	ENSP00000300227:R472W	R	-	1	2	C18orf34	29079386	0.600000	0.26899	0.438000	0.26821	0.013000	0.08279	1.203000	0.32284	0.400000	0.25396	-0.375000	0.07067	CGG	G|0.998;A|0.002	0.002	strong		0.234	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
CCAR1	55749	hgsc.bcm.edu	37	10	70513614	70513614	+	Missense_Mutation	SNP	G	G	T	rs368721550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:70513614G>T	ENST00000265872.6	+	11	1243	c.1124G>T	c.(1123-1125)aGt>aTt	p.S375I	SNORD98_ENST00000408255.1_RNA|CCAR1_ENST00000535016.1_Missense_Mutation_p.S360I|CCAR1_ENST00000543719.1_Missense_Mutation_p.S360I	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	375					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TTCAGTCCCAGTTGTGACATG	0.328																																					p.S375I		Atlas-SNP	.											.	CCAR1	118	.	0			c.G1124T						PASS	.	G	ILE/SER	0,4406		0,0,2203	141.0	144.0	143.0		1124	5.9	1.0	10		143	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCAR1	NM_018237.2	142	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	375/1151	70513614	1,13005	2203	4300	6503	SO:0001583	missense	55749	exon11			GTCCCAGTTGTGA	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.1124G>T	10.37:g.70513614G>T	ENSP00000265872:p.Ser375Ile	122.0	0.0	0		109.0	55.0	0.504587	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	37	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261009	0.59431	0.0	1.16E-4	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.23950	1.89;1.88;1.88;1.88;1.89;1.89	5.95	5.95	0.96441	.	0.076157	0.85682	D	0.000000	T	0.23133	0.0559	L	0.28192	0.835	0.43133	D	0.994878	P;D;B	0.56521	0.729;0.976;0.1	B;B;B	0.41988	0.372;0.361;0.043	T	0.01021	-1.1478	10	0.38643	T	0.18	-14.4237	20.3886	0.98946	0.0:0.0:1.0:0.0	.	360;375;349	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	I	375;360;360;360;349;180	ENSP00000265872:S375I;ENSP00000441820:S360I;ENSP00000445254:S360I;ENSP00000439252:S360I;ENSP00000438610:S349I;ENSP00000439642:S180I	ENSP00000265872:S375I	S	+	2	0	CCAR1	70183620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.053000	0.57427	2.810000	0.96702	0.650000	0.86243	AGT	.	.	none		0.328	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	
LRRIQ3	127255	hgsc.bcm.edu	37	1	74648375	74648375	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:74648375A>G	ENST00000395089.1	-	2	419	c.420T>C	c.(418-420)taT>taC	p.Y140Y	LRRIQ3_ENST00000370911.3_Silent_p.Y140Y|LRRIQ3_ENST00000370909.2_Intron|LRRIQ3_ENST00000354431.4_Silent_p.Y140Y			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	140	LRRCT.									NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						GAACATGTCTATATCCTTTTT	0.373																																					p.Y140Y		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.T420C						PASS	.						115.0	111.0	112.0					1																	74648375		2203	4298	6501	SO:0001819	synonymous_variant	127255	exon3			ATGTCTATATCCT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.420T>C	1.37:g.74648375A>G		68.0	0.0	0		83.0	26.0	0.313253	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																			.	.	none		0.373	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
ABHD5	51099	hgsc.bcm.edu	37	3	43743773	43743773	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:43743773A>C	ENST00000458276.2	+	3	323	c.200A>C	c.(199-201)aAg>aCg	p.K67T		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	67					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		TGGACACTGAAGTTCTCTCAT	0.373																																					p.K67T		Atlas-SNP	.											ABHD5,NS,carcinoma,-1,1	ABHD5	33	1	0			c.A200C						PASS	.						96.0	99.0	98.0					3																	43743773		2203	4300	6503	SO:0001583	missense	51099	exon3			CACTGAAGTTCTC	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"""Abhydrolase domain containing"""	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.200A>C	3.37:g.43743773A>C	ENSP00000390849:p.Lys67Thr	81.0	0.0	0		63.0	20.0	0.31746	NM_016006	B2R9K0|Q9Y369	Missense_Mutation	SNP	ENST00000458276.2	37	CCDS2711.1	.	.	.	.	.	.	.	.	.	.	A	2.866	-0.235130	0.05983	.	.	ENSG00000011198	ENST00000456453;ENST00000458276;ENST00000454293	T;D;T	0.82344	-0.96;-1.6;-0.57	5.96	4.78	0.61160	.	0.270286	0.39834	N	0.001247	T	0.66848	0.2831	L	0.31476	0.935	0.25387	N	0.988565	B	0.02656	0.0	B	0.08055	0.003	T	0.51505	-0.8697	10	0.02654	T	1	-23.1746	6.1406	0.20257	0.5209:0.2363:0.0:0.2428	.	67	Q8WTS1	ABHD5_HUMAN	T	26;67;26	ENSP00000391582:K26T;ENSP00000390849:K67T;ENSP00000412014:K26T	ENSP00000412014:K26T	K	+	2	0	ABHD5	43718777	0.761000	0.28439	1.000000	0.80357	0.997000	0.91878	1.463000	0.35277	1.038000	0.40049	0.528000	0.53228	AAG	.	.	none		0.373	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006	
URB1	9875	hgsc.bcm.edu	37	21	33726303	33726303	+	Silent	SNP	C	C	T	rs200555493		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33726303C>T	ENST00000382751.3	-	18	2470	c.2355G>A	c.(2353-2355)gcG>gcA	p.A785A		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	785						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						CAGGGACTACCGCACTGAATG	0.537																																					p.A785A		Atlas-SNP	.											.	URB1	176	.	0			c.G2355A						PASS	.	C		1,1383		0,1,691	156.0	132.0	139.0		2355	-11.7	0.0	21		139	2,3180		0,2,1589	no	coding-synonymous	URB1	NM_014825.2		0,3,2280	TT,TC,CC		0.0629,0.0723,0.0657		785/2272	33726303	3,4563	692	1591	2283	SO:0001819	synonymous_variant	9875	exon18			GACTACCGCACTG	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.2355G>A	21.37:g.33726303C>T		95.0	0.0	0		141.0	63.0	0.446809	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			C|0.998;T|0.002	0.002	weak		0.537	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:125928395A>G	ENST00000409134.3	-	3	492	c.273T>C	c.(271-273)acT>acC	p.T91T	ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000447989.2_Silent_p.T118T	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	91					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		CTTTCTTTACAGTTTCTTCAT	0.368													A|||	302	0.0603035	0.1717	0.0274	5008	,	,		18399	0.0		0.0288	False		,,,				2504	0.0276				p.T118T		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.T354C						PASS	.	A	,,	657,3749	278.1+/-274.1	42,573,1588	111.0	105.0	107.0		273,189,354	-9.2	0.1	5	dbSNP_129	107	214,8386	88.9+/-151.2	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	,,	44,783,5676	GG,GA,AA		2.4884,14.9115,6.6969	,,	91/540,63/512,118/503	125928395	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	501	exon3			CTTTACAGTTTCT	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"""Aldehyde dehydrogenases"""	877	protein-coding gene	gene with protein product	"""antiquitin 1"", ""26g turgor protein homolog"", ""alpha-aminoadipic semialdehyde dehydrogenase"", ""alpha-AASA dehydrogenase"", ""delta1-piperideine-6-carboxylate dehydrogenease"", ""P6c dehydrogenase"""	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.273T>C	5.37:g.125928395A>G		106.0	0.0	0		96.0	51.0	0.53125	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																			A|0.941;G|0.059	0.059	strong		0.368	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182	
ZPLD1	131368	hgsc.bcm.edu	37	3	102171858	102171858	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:102171858C>A	ENST00000491959.1	+	10	1084	c.202C>A	c.(202-204)Ctg>Atg	p.L68M	ZPLD1_ENST00000466937.1_Missense_Mutation_p.L68M|ZPLD1_ENST00000306176.1_Missense_Mutation_p.L84M			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	68	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						GGAAACAGATCTGGCACTGAA	0.438																																					p.L84M		Atlas-SNP	.											.	ZPLD1	82	.	0			c.C250A						PASS	.						101.0	97.0	98.0					3																	102171858		2203	4300	6503	SO:0001583	missense	131368	exon3			ACAGATCTGGCAC	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.202C>A	3.37:g.102171858C>A	ENSP00000420265:p.Leu68Met	143.0	0.0	0		118.0	44.0	0.372881	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		.	.	.	.	.	.	.	.	.	.	C	16.88	3.244144	0.59103	.	.	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.84589	-1.87;-1.87;-1.87	5.99	4.18	0.49190	Zona pellucida sperm-binding protein (3);	0.065284	0.64402	D	0.000006	T	0.81408	0.4816	L	0.39020	1.185	0.58432	D	0.999992	P;P	0.48694	0.875;0.914	B;P	0.47206	0.241;0.541	T	0.81656	-0.0834	10	0.52906	T	0.07	-1.7625	11.6233	0.51130	0.0:0.8362:0.0:0.1638	.	84;68	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	M	68;84;68	ENSP00000420265:L68M;ENSP00000307801:L84M;ENSP00000418253:L68M	ENSP00000307801:L84M	L	+	1	2	ZPLD1	103654548	0.947000	0.32204	1.000000	0.80357	0.994000	0.84299	0.155000	0.16362	2.840000	0.97914	0.655000	0.94253	CTG	.	.	none		0.438	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
FOXA2	3170	hgsc.bcm.edu	37	20	22563684	22563684	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:22563684C>T	ENST00000377115.4	-	3	359	c.178G>A	c.(178-180)Gcg>Acg	p.A60T	FOXA2_ENST00000419308.2_Missense_Mutation_p.A66T	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	60	Transactivation domain 1. {ECO:0000250}.				adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					ATGGAGCCCGCGCTCATGTTG	0.692																																					p.A66T		Atlas-SNP	.											.	FOXA2	48	.	0			c.G196A						PASS	.						48.0	50.0	50.0					20																	22563684		2200	4291	6491	SO:0001583	missense	3170	exon2			AGCCCGCGCTCAT	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"""Forkhead boxes"""	5022	protein-coding gene	gene with protein product		600288	"""hepatocyte nuclear factor 3, beta"""	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.178G>A	20.37:g.22563684C>T	ENSP00000366319:p.Ala60Thr	83.0	0.0	0		68.0	27.0	0.397059	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	C	4.203	0.036488	0.08148	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993	D;D;D	0.90504	-2.68;-2.68;-2.68	4.42	2.29	0.28610	Fork-head N-terminal (1);	.	.	.	.	D	0.85008	0.5599	L	0.50333	1.59	0.53005	D	0.999967	B;B	0.10296	0.003;0.003	B;B	0.08055	0.002;0.003	T	0.76610	-0.2896	9	0.22706	T	0.39	.	8.3158	0.32100	0.0:0.7519:0.1567:0.0914	.	60;66	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	T	60;60;66	ENSP00000366319:A60T;ENSP00000400341:A60T;ENSP00000315955:A66T	ENSP00000315955:A66T	A	-	1	0	FOXA2	22511684	0.376000	0.25098	0.994000	0.49952	0.994000	0.84299	1.624000	0.37018	0.827000	0.34685	0.467000	0.42956	GCG	.	.	none		0.692	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1		
CALHM3	119395	hgsc.bcm.edu	37	10	105233301	105233301	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105233301G>A	ENST00000369783.4	-	3	911	c.704C>T	c.(703-705)gCg>gTg	p.A235V		NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	235					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						GAAGTCCCGCGCATGCTCACA	0.642																																					p.A235V		Atlas-SNP	.											.	CALHM3	46	.	0			c.C704T						PASS	.						8.0	9.0	9.0					10																	105233301		692	1586	2278	SO:0001583	missense	119395	exon3			TCCCGCGCATGCT	BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.704C>T	10.37:g.105233301G>A	ENSP00000358798:p.Ala235Val	88.0	0.0	0		54.0	28.0	0.518519	NM_001129742	Q5W090|Q8IXR2	Missense_Mutation	SNP	ENST00000369783.4	37	CCDS44476.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226863	0.95173	.	.	ENSG00000183128	ENST00000369783	T	0.30182	1.54	5.67	5.67	0.87782	.	0.137730	0.48286	D	0.000199	T	0.58906	0.2155	M	0.80183	2.485	0.54753	D	0.999989	D	0.89917	1.0	D	0.78314	0.991	T	0.62798	-0.6778	10	0.87932	D	0	-5.7687	16.265	0.82571	0.0:0.1414:0.8586:0.0	.	235	Q86XJ0-2	.	V	235	ENSP00000358798:A235V	ENSP00000358798:A235V	A	-	2	0	CALHM3	105223291	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.236000	0.78154	2.677000	0.91161	0.462000	0.41574	GCG	.	.	none		0.642	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
KIAA0226	9711	hgsc.bcm.edu	37	3	197427584	197427584	+	Silent	SNP	G	G	A	rs368476866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:197427584G>A	ENST00000296343.5	-	7	1160	c.1161C>T	c.(1159-1161)tcC>tcT	p.S387S	KIAA0226_ENST00000389665.5_Silent_p.S387S|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000273582.5_Silent_p.S327S|KIAA0226_ENST00000449205.1_Silent_p.S387S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	387	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		CTGAGAAGCTGGACCTGCGGA	0.597																																					p.S387S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.C1161T						PASS	.	G	,	0,4100		0,0,2050	68.0	72.0	71.0		981,1161	4.1	1.0	3		71	6,8382		0,6,4188	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	0,6,6238	AA,AG,GG		0.0715,0.0,0.048	,	327/928,387/973	197427584	6,12482	2050	4194	6244	SO:0001819	synonymous_variant	9711	exon7			GAAGCTGGACCTG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1161C>T	3.37:g.197427584G>A		97.0	0.0	0		132.0	63.0	0.477273	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.751|9.751	1.167581|1.167581	0.21621|0.21621	0.0|0.0	7.15E-4|7.15E-4	ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000413360	.|.	.|.	.|.	5.85|5.85	4.05|4.05	0.47172|0.47172	.|.	.|.	.|.	.|.	.|.	T|.	0.60907|.	0.2305|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.56727|.	-0.7931|.	4|.	.|.	.|.	.|.	.|.	9.9492|9.9492	0.41628|0.41628	0.1594:0.0:0.8406:0.0|0.1594:0.0:0.8406:0.0	.|.	.|.	.|.	.|.	L|X	146|366	.|.	.|.	P|Q	-|-	2|1	0|0	KIAA0226|KIAA0226	198911981|198911981	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	2.081000|2.081000	0.41596|0.41596	0.791000|0.791000	0.33826|0.33826	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.	weak		0.597	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ATAD3C	219293	hgsc.bcm.edu	37	1	1403848	1403848	+	Missense_Mutation	SNP	C	C	G	rs370109447		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1403848C>G	ENST00000378785.2	+	12	2169	c.1174C>G	c.(1174-1176)Cag>Gag	p.Q392E		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	392							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCAGCACCAGCAGATGATGCG	0.657																																					p.Q392E		Atlas-SNP	.											.	ATAD3C	23	.	0			c.C1174G						PASS	.	C	GLU/GLN	0,4406		0,0,2203	32.0	35.0	34.0		1174	1.5	1.0	1		34	2,8588		0,2,4293	no	missense	ATAD3C	NM_001039211.2	29	0,2,6496	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging	392/412	1403848	2,12994	2203	4295	6498	SO:0001583	missense	219293	exon12			CACCAGCAGATGA	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.1174C>G	1.37:g.1403848C>G	ENSP00000368062:p.Gln392Glu	196.0	0.0	0		172.0	80.0	0.465116	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	.	.	.	.	.	.	.	.	.	.	.	9.977	1.227126	0.22542	0.0	2.33E-4	ENSG00000215915	ENST00000378785	D	0.94576	-3.46	1.47	1.47	0.22746	.	.	.	.	.	D	0.92883	0.7736	M	0.81341	2.54	0.54753	D	0.999986	B	0.34015	0.435	B	0.32149	0.141	D	0.92131	0.5712	9	0.56958	D	0.05	.	10.4293	0.44398	0.0:1.0:0.0:0.0	.	392	Q5T2N8	ATD3C_HUMAN	E	392	ENSP00000368062:Q392E	ENSP00000368062:Q392E	Q	+	1	0	ATAD3C	1393711	1.000000	0.71417	0.997000	0.53966	0.055000	0.15305	5.266000	0.65525	1.135000	0.42183	0.194000	0.17425	CAG	.	.	none		0.657	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
MCM6	4175	hgsc.bcm.edu	37	2	136602196	136602196	+	Silent	SNP	G	G	A	rs4988270	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:136602196G>A	ENST00000264156.2	-	16	2328	c.2268C>T	c.(2266-2268)atC>atT	p.I756I	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	756					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		TCTCTGATTCGATTTCCTTCA	0.378													G|||	9	0.00179712	0.0	0.0	5008	,	,		20306	0.0		0.007	False		,,,				2504	0.002				p.I756I	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.C2268T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	140.0	135.0	137.0		2268	-8.5	0.8	2	dbSNP_113	137	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	MCM6	NM_005915.4		0,43,6460	AA,AG,GG		0.4651,0.0681,0.3306		756/822	136602196	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	4175	exon16			TGATTCGATTTCC		CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"""MIS5 homolog (S.pombe)"""	601806	"""minichromosome maintenance deficient (mis5, S. pombe) 6"", ""MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)"", ""minichromosome maintenance deficient 6 homolog (S. cerevisiae)"""				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.2268C>T	2.37:g.136602196G>A		48.0	0.0	0		54.0	10.0	0.185185	NM_005915	B2R6H2|Q13504|Q99859	Silent	SNP	ENST00000264156.2	37	CCDS2179.1																																																																																			G|0.997;A|0.003	0.003	strong		0.378	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915	
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219824731G>C	ENST00000302625.4	+	1	355	c.189G>C	c.(187-189)gcG>gcC	p.A63A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	63					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCTCGGCGCTCACCTGGA	0.716													G|||	163	0.0325479	0.0061	0.0375	5008	,	,		7620	0.0179		0.0398	False		,,,				2504	0.0726				p.A63A		Atlas-SNP	.											.	CDK5R2	17	.	0			c.G189C						PASS	.	G		22,4302		2,18,2142	10.0	14.0	13.0		189	2.5	1.0	2	dbSNP_131	13	213,8313		1,211,4051	no	coding-synonymous	CDK5R2	NM_003936.3		3,229,6193	CC,CG,GG		2.4982,0.5088,1.8288		63/368	219824731	235,12615	2162	4263	6425	SO:0001819	synonymous_variant	8941	exon1			CTCGGCGCTCACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"""neuronal CDK5 activator isoform"""	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.189G>C	2.37:g.219824731G>C		26.0	0.0	0		22.0	12.0	0.545455	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																			G|0.972;C|0.028	0.028	strong		0.716	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936	
TXNDC11	51061	hgsc.bcm.edu	37	16	11785486	11785486	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11785486G>A	ENST00000356957.3	-	9	1748	c.1641C>T	c.(1639-1641)atC>atT	p.I547I	TXNDC11_ENST00000570917.1_5'Flank|TXNDC11_ENST00000283033.5_Silent_p.I520I			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	547					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GTTCAGAGTCGATGAAGCCTG	0.473																																					p.I520I		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C1560T						PASS	.						121.0	112.0	115.0					16																	11785486		2197	4300	6497	SO:0001819	synonymous_variant	51061	exon8			AGAGTCGATGAAG	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.1641C>T	16.37:g.11785486G>A		46.0	0.0	0		62.0	33.0	0.532258	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	37																																																																																				.	.	none		0.473	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
PRRT3	285368	hgsc.bcm.edu	37	3	9989028	9989028	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9989028G>A	ENST00000412055.1	-	4	1958	c.1829C>T	c.(1828-1830)gCg>gTg	p.A610V	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	610						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						AGCCACGGCCGCGCCCCAGGC	0.711																																					p.A610V		Atlas-SNP	.											.	PRRT3	35	.	0			c.C1829T						PASS	.						9.0	11.0	11.0					3																	9989028		1927	3904	5831	SO:0001583	missense	285368	exon4			ACGGCCGCGCCCC	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1829C>T	3.37:g.9989028G>A	ENSP00000392511:p.Ala610Val	6.0	0.0	0		17.0	5.0	0.294118	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440426	0.43326	.	.	ENSG00000163704	ENST00000412055	T	0.14640	2.49	4.43	4.43	0.53597	.	0.183502	0.37623	N	0.002019	T	0.10252	0.0251	N	0.14661	0.345	0.80722	D	1	D	0.61080	0.989	P	0.49085	0.6	T	0.12372	-1.0550	9	.	.	.	-20.0165	8.2211	0.31541	0.106:0.0:0.894:0.0	.	610	Q5FWE3	PRRT3_HUMAN	V	610	ENSP00000392511:A610V	.	A	-	2	0	PRRT3	9964028	0.999000	0.42202	0.934000	0.37439	0.981000	0.71138	4.195000	0.58400	2.298000	0.77334	0.462000	0.41574	GCG	.	.	none		0.711	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
TRAK1	22906	hgsc.bcm.edu	37	3	42251321	42251321	+	Missense_Mutation	SNP	C	C	T	rs375255978		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42251321C>T	ENST00000327628.5	+	14	2207	c.1807C>T	c.(1807-1809)Ccc>Tcc	p.P603S	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.P545S|TRAK1_ENST00000341421.3_Missense_Mutation_p.P545S	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	603					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CATCCTGGACCCCCGGCCCGG	0.587																																					p.P603S	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1807T						PASS	.	C	SER/PRO,SER/PRO	0,4406		0,0,2203	75.0	76.0	76.0		1807,1633	5.5	1.0	3		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TRAK1	NM_001042646.1,NM_014965.3	74,74	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	603/954,545/687	42251321	1,13005	2203	4300	6503	SO:0001583	missense	22906	exon14			CTGGACCCCCGGC		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1807C>T	3.37:g.42251321C>T	ENSP00000328998:p.Pro603Ser	55.0	0.0	0		60.0	24.0	0.4	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833399	0.50951	0.0	1.16E-4	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175;ENST00000341421	T;T;T	0.09073	3.05;3.06;3.02	5.49	5.49	0.81192	.	0.062197	0.64402	D	0.000005	T	0.11580	0.0282	L	0.39898	1.24	0.38529	D	0.948939	P;P;P;P;B	0.52316	0.524;0.728;0.851;0.952;0.105	B;B;B;B;B	0.43916	0.095;0.196;0.253;0.436;0.038	T	0.03221	-1.1059	10	0.46703	T	0.11	.	18.3674	0.90396	0.0:1.0:0.0:0.0	.	529;545;603;545;603	B7Z218;C9JC32;B7Z347;Q9UPV9-2;Q9UPV9	.;.;.;.;TRAK1_HUMAN	S	603;603;545;545	ENSP00000328998:P603S;ENSP00000379478:P545S;ENSP00000340702:P545S	ENSP00000328998:P603S	P	+	1	0	TRAK1	42226325	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.457000	0.35212	2.571000	0.86741	0.655000	0.94253	CCC	.	.	weak		0.587	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136320665	136320665	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136320665T>C	ENST00000371929.3	+	25	3952	c.3508T>C	c.(3508-3510)Tcc>Ccc	p.S1170P	ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Intron|ADAMTS13_ENST00000356589.2_Intron|ADAMTS13_ENST00000371910.1_5'Flank	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1170					cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CCTGCTCTTCTCCCCGGCTCC	0.687																																					p.S1170P		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.T3508C						PASS	.						29.0	37.0	34.0					9																	136320665		2187	4277	6464	SO:0001583	missense	11093	exon25			CTCTTCTCCCCGG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.3508T>C	9.37:g.136320665T>C	ENSP00000360997:p.Ser1170Pro	47.0	0.0	0		35.0	19.0	0.542857	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	T	8.768	0.925251	0.18056	.	.	ENSG00000160323	ENST00000371929	D	0.81996	-1.56	5.21	1.62	0.23740	.	.	.	.	.	T	0.69949	0.3168	L	0.31294	0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53143	-0.8480	8	.	.	.	.	6.5444	0.22398	0.0:0.4072:0.0:0.5928	.	1170	Q76LX8	ATS13_HUMAN	P	1170	ENSP00000360997:S1170P	.	S	+	1	0	ADAMTS13	135310486	0.000000	0.05858	0.023000	0.16930	0.035000	0.12851	-0.151000	0.10175	0.310000	0.22990	0.459000	0.35465	TCC	.	.	none		0.687	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
DAGLA	747	hgsc.bcm.edu	37	11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	rs117050893	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:61511794C>G	ENST00000257215.5	+	20	3078	c.2962C>G	c.(2962-2964)Ctc>Gtc	p.L988V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	988					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GGGCATCTCACTCTCGCCCTC	0.667													C|||	33	0.00658946	0.0	0.0331	5008	,	,		16155	0.002		0.006	False		,,,				2504	0.002				p.L988V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2962G						PASS	.	C	VAL/LEU	18,4386	24.3+/-50.5	0,18,2184	56.0	62.0	60.0		2962	2.0	0.0	11	dbSNP_132	60	38,8560	25.7+/-73.6	0,38,4261	yes	missense	DAGLA	NM_006133.2	32	0,56,6445	GG,GC,CC		0.442,0.4087,0.4307	benign	988/1043	61511794	56,12946	2202	4299	6501	SO:0001583	missense	747	exon20			ATCTCACTCTCGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2962C>G	11.37:g.61511794C>G	ENSP00000257215:p.Leu988Val	54.0	0.0	0		50.0	21.0	0.42	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	21	0.009615384615384616	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	5	0.006596306068601583	C	5.197	0.221827	0.09863	0.004087	0.00442	ENSG00000134780	ENST00000257215	T	0.25085	1.82	4.03	1.95	0.26073	.	0.158981	0.41097	D	0.000955	T	0.01905	0.0060	N	0.03608	-0.345	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.32268	-0.9913	10	0.17369	T	0.5	-26.7772	8.6434	0.33991	0.0:0.5927:0.3026:0.1048	.	988	Q9Y4D2	DGLA_HUMAN	V	988	ENSP00000257215:L988V	ENSP00000257215:L988V	L	+	1	0	DAGLA	61268370	0.954000	0.32549	0.008000	0.14137	0.636000	0.38137	1.749000	0.38319	0.815000	0.34398	0.462000	0.41574	CTC	C|0.994;G|0.006	0.006	strong		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
UBOX5	22888	hgsc.bcm.edu	37	20	3102636	3102636	+	Missense_Mutation	SNP	G	G	C	rs148731933	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3102636G>C	ENST00000217173.2	-	3	1120	c.649C>G	c.(649-651)Ctg>Gtg	p.L217V	UBOX5_ENST00000348031.2_Missense_Mutation_p.L217V|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						TCCTGAGGCAGGTTCTCTGAG	0.607																																					p.L217V		Atlas-SNP	.											UBOX5,NS,carcinoma,+2,1	UBOX5	47	1	0			c.C649G						PASS	.	G	VAL/LEU,VAL/LEU	1,4405	2.1+/-5.4	0,1,2202	48.0	43.0	45.0		649,649	2.2	0.0	20	dbSNP_134	45	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	UBOX5	NM_014948.2,NM_199415.1	32,32	0,7,6496	CC,CG,GG		0.0698,0.0227,0.0538	benign,benign	217/542,217/488	3102636	7,12999	2203	4300	6503	SO:0001583	missense	22888	exon3			GAGGCAGGTTCTC	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"""RING-type (C3HC4) zinc fingers"", ""U-box domain containing"""	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.649C>G	20.37:g.3102636G>C	ENSP00000217173:p.Leu217Val	49.0	0.0	0		54.0	27.0	0.5	NM_014948		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	1.639	-0.517024	0.04171	2.27E-4	6.98E-4	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.35048	1.33;1.33	5.42	2.19	0.27852	.	0.745856	0.12057	U	0.503558	T	0.20333	0.0489	N	0.17082	0.46	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.003	T	0.17379	-1.0371	10	0.41790	T	0.15	-0.1066	5.4175	0.16382	0.0649:0.227:0.4742:0.2339	.	217;217;217	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	V	217	ENSP00000217173:L217V;ENSP00000311726:L217V	ENSP00000217173:L217V	L	-	1	2	UBOX5	3050636	0.015000	0.18098	0.036000	0.18154	0.082000	0.17680	0.438000	0.21559	0.617000	0.30160	0.563000	0.77884	CTG	G|1.000;C|0.000	0.000	strong		0.607	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948	
MUC4	4585	hgsc.bcm.edu	37	3	195506159	195506159	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195506159G>C	ENST00000463781.3	-	2	12751	c.12292C>G	c.(12292-12294)Cct>Gct	p.P4098A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4098A|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGGTGAGAGGAAGAGGGGTG	0.582																																					p.P4098A		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12292G						PASS	.						24.0	12.0	16.0					3																	195506159		569	1407	1976	SO:0001583	missense	4585	exon2			TGAGAGGAAGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12292C>G	3.37:g.195506159G>C	ENSP00000417498:p.Pro4098Ala	80.0	0.0	0		26.0	19.0	0.730769	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.888	0.348046	0.11126	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26957	1.72;1.7	.	.	.	.	.	.	.	.	T	0.11793	0.0287	N	0.19112	0.55	0.09310	N	0.999994	B	0.31837	0.342	B	0.25405	0.06	T	0.23154	-1.0196	7	.	.	.	.	2.9304	0.05797	0.3911:0.0:0.6089:0.0	.	3970	E7ESK3	.	A	4098	ENSP00000417498:P4098A;ENSP00000420243:P4098A	.	P	-	1	0	MUC4	196990938	0.001000	0.12720	0.005000	0.12908	0.053000	0.15095	0.202000	0.17295	0.488000	0.27723	0.064000	0.15345	CCT	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NLRP12	91662	hgsc.bcm.edu	37	19	54313944	54313944	+	Silent	SNP	A	A	C	rs142063194	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54313944A>C	ENST00000324134.6	-	3	1137	c.969T>G	c.(967-969)ctT>ctG	p.L323L	NLRP12_ENST00000391772.1_Silent_p.L323L|NLRP12_ENST00000391773.1_Silent_p.L323L|NLRP12_ENST00000354278.3_Silent_p.L323L|NLRP12_ENST00000391775.3_Silent_p.L323L|NLRP12_ENST00000535162.1_Silent_p.L323L|NLRP12_ENST00000345770.5_Silent_p.L323L|NLRP12_ENST00000351894.4_Silent_p.L323L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	323	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGCTGTTAAGAAGCAGCTCCG	0.562													A|||	22	0.00439297	0.0	0.0086	5008	,	,		17335	0.0		0.007	False		,,,				2504	0.0092				p.S323R		Atlas-SNP	.											.	NLRP12	236	.	0			c.C969G						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	49.0	52.0	51.0		969	-8.6	0.0	19	dbSNP_134	51	117,8483	61.0+/-122.8	0,117,4183	no	coding-synonymous	NLRP12	NM_144687.2		0,126,6377	CC,CA,AA		1.3605,0.2043,0.9688		323/1062	54313944	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	91662	exon3			GTTAAGAAGCAGC	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.969T>G	19.37:g.54313944A>C		51.0	0.0	0		51.0	27.0	0.529412	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																			A|0.991;C|0.009	0.009	strong		0.562	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
ZNF417	147687	hgsc.bcm.edu	37	19	58420416	58420416	+	Silent	SNP	G	G	A	rs150518835	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58420416G>A	ENST00000312026.5	-	3	1394	c.1230C>T	c.(1228-1230)tgC>tgT	p.C410C	ZNF417_ENST00000536263.1_Silent_p.C211C|ZNF417_ENST00000595559.1_Silent_p.C409C|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CACATTCCTTGCACTCATAGG	0.453													G|||	37	0.00738818	0.0	0.0086	5008	,	,		23472	0.0		0.0298	False		,,,				2504	0.001				p.C410C		Atlas-SNP	.											.	ZNF417	44	.	0			c.C1230T						PASS	.	G		24,4382		0,24,2179	108.0	100.0	103.0		1230	-1.5	0.0	19	dbSNP_134	103	215,8385		5,205,4090	no	coding-synonymous	ZNF417	NM_152475.2		5,229,6269	AA,AG,GG		2.5,0.5447,1.8376		410/576	58420416	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	147687	exon3			TTCCTTGCACTCA	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1230C>T	19.37:g.58420416G>A		79.0	0.0	0		80.0	25.0	0.3125	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
FAM208A	23272	hgsc.bcm.edu	37	3	56667896	56667896	+	Missense_Mutation	SNP	G	G	T	rs200904014	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:56667896G>T	ENST00000493960.2	-	18	2933	c.2923C>A	c.(2923-2925)Cag>Aag	p.Q975K	FAM208A_ENST00000355628.5_Intron|FAM208A_ENST00000431842.2_Intron	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	975							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						GATGGAAACTGGTAATCAGAA	0.507													G|||	27	0.00539137	0.0	0.0014	5008	,	,		16957	0.0		0.003	False		,,,				2504	0.0235				p.Q975K		Atlas-SNP	.											.	FAM208A	113	.	0			c.C2923A						PASS	.	G	LYS/GLN,	1,4405	2.1+/-5.4	0,1,2202	26.0	24.0	25.0		2923,	4.7	1.0	3		25	15,8585	9.8+/-36.6	0,15,4285	yes	missense,intron	FAM208A	NM_001112736.1,NM_015224.3	53,	0,16,6487	TT,TG,GG		0.1744,0.0227,0.123	benign,	975/1513,	56667896	16,12990	2203	4300	6503	SO:0001583	missense	23272	exon18			GAAACTGGTAATC	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.2923C>A	3.37:g.56667896G>T	ENSP00000417509:p.Gln975Lys	97.0	0.0	0		67.0	36.0	0.537313	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.13	2.743511	0.49151	2.27E-4	0.001744	ENSG00000163946	ENST00000493960	T	0.11604	2.76	5.62	4.69	0.59074	.	.	.	.	.	T	0.08403	0.0209	L	0.36672	1.1	0.80722	D	1	B;B	0.28082	0.2;0.067	B;B	0.24155	0.051;0.012	T	0.04593	-1.0940	9	0.02654	T	1	.	15.6619	0.77193	0.0:0.0:0.8623:0.1377	.	975;975	Q9UK61-3;Q9UK61	.;F208A_HUMAN	K	975	ENSP00000417509:Q975K	ENSP00000417509:Q975K	Q	-	1	0	C3orf63	56642936	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.602000	0.61098	2.801000	0.96364	0.650000	0.86243	CAG	G|0.999;T|0.001	0.001	strong		0.507	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000538752.1_Silent_p.S44S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000592625.1_Silent_p.S24S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150.0	152.0	151.0					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.72G>C	19.37:g.12087921G>C		137.0	1.0	0.00729927		96.0	9.0	0.09375	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
ICE1	23379	hgsc.bcm.edu	37	5	5441314	5441314	+	Missense_Mutation	SNP	A	A	G	rs72646675	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:5441314A>G	ENST00000296564.7	+	5	509	c.287A>G	c.(286-288)aAa>aGa	p.K96R	KIAA0947_ENST00000512608.1_3'UTR	NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		96					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GGATCTTTAAAAGCAGAGCTA	0.358													A|||	3	0.000599042	0.0	0.0	5008	,	,		15735	0.0		0.003	False		,,,				2504	0.0				p.K96R		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A287G						PASS	.	A	ARG/LYS	1,3585		0,1,1792	26.0	25.0	25.0		287	4.6	1.0	5	dbSNP_130	25	12,8084		0,12,4036	yes	missense	KIAA0947	NM_015325.1	26	0,13,5828	GG,GA,AA		0.1482,0.0279,0.1113	possibly-damaging	96/2267	5441314	13,11669	1793	4048	5841	SO:0001583	missense	23379	exon5			CTTTAAAAGCAGA																												ENST00000296564.7:c.287A>G	5.37:g.5441314A>G	ENSP00000296564:p.Lys96Arg	201.0	0.0	0		203.0	93.0	0.458128	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	20.5	3.995633	0.74703	2.79E-4	0.001482	ENSG00000164151	ENST00000296564	T	0.14266	2.52	5.78	4.61	0.57282	.	0.070003	0.56097	D	0.000040	T	0.20170	0.0485	L	0.29908	0.895	0.25024	N	0.991316	D	0.64830	0.994	D	0.65010	0.931	T	0.05338	-1.0891	10	0.35671	T	0.21	-37.5493	8.4511	0.32871	0.9118:0.0:0.0882:0.0	.	96	Q9Y2F5	K0947_HUMAN	R	96	ENSP00000296564:K96R	ENSP00000296564:K96R	K	+	2	0	KIAA0947	5494314	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	2.791000	0.47829	1.014000	0.39417	0.477000	0.44152	AAA	A|0.999;G|0.001	0.001	strong		0.358	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
TSC22D1	8848	hgsc.bcm.edu	37	13	45149973	45149973	+	Missense_Mutation	SNP	G	G	A	rs140514784		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:45149973G>A	ENST00000458659.2	-	1	728	c.238C>T	c.(238-240)Ccg>Tcg	p.P80S	TSC22D1_ENST00000501704.2_Missense_Mutation_p.P80S|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	80	Pro-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TGTGGAGGCGGAGGCTGTGGT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		17451	0.0		0.0	False		,,,				2504	0.001				p.P80S		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C238T						PASS	.	G	SER/PRO	4,4402	8.1+/-20.4	0,4,2199	58.0	58.0	58.0		238	4.2	1.0	13	dbSNP_134	58	22,8578	15.3+/-51.7	0,22,4278	yes	missense	TSC22D1	NM_183422.3	74	0,26,6477	AA,AG,GG		0.2558,0.0908,0.1999	possibly-damaging	80/1074	45149973	26,12980	2203	4300	6503	SO:0001583	missense	8848	exon1			GAGGCGGAGGCTG	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.238C>T	13.37:g.45149973G>A	ENSP00000397435:p.Pro80Ser	128.0	0.0	0		202.0	151.0	0.747525	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829773	0.71258	9.08E-4	0.002558	ENSG00000102804	ENST00000458659;ENST00000501704;ENST00000493016	T	0.32272	1.46	4.23	4.23	0.50019	.	0.000000	0.48286	D	0.000189	T	0.18087	0.0434	N	0.14661	0.345	0.33605	D	0.602832	P;P	0.39809	0.573;0.689	B;B	0.36666	0.23;0.186	T	0.28396	-1.0045	10	0.52906	T	0.07	.	11.7357	0.51763	0.0:0.0:0.8231:0.1769	.	80;80	B3KRL7;Q15714	.;T22D1_HUMAN	S	80	ENSP00000397435:P80S	ENSP00000397435:P80S	P	-	1	0	TSC22D1	44047973	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.180000	0.71981	2.337000	0.79520	0.561000	0.74099	CCG	G|0.999;A|0.001	0.001	strong		0.592	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
TET3	200424	hgsc.bcm.edu	37	2	74320089	74320089	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:74320089C>T	ENST00000409262.3	+	6	2695	c.2695C>T	c.(2695-2697)Cga>Tga	p.R899*		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	899					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCTGTACAAGCGACTGGCCCC	0.612																																					p.R899X		Atlas-SNP	.											.	TET3	101	.	0			c.C2695T						PASS	.						19.0	20.0	20.0					2																	74320089		1934	4130	6064	SO:0001587	stop_gained	200424	exon6			TACAAGCGACTGG		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.2695C>T	2.37:g.74320089C>T	ENSP00000386869:p.Arg899*	202.0	0.0	0		144.0	74.0	0.513889	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Nonsense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	C	39	7.569305	0.98365	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	.	.	.	4.61	2.62	0.31277	.	0.543822	0.18552	N	0.137888	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7839	0.52030	0.4338:0.5662:0.0:0.0	.	.	.	.	X	899	.	ENSP00000233310:R899X	R	+	1	2	TET3	74173597	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.062000	0.41413	1.240000	0.43803	0.655000	0.94253	CGA	.	.	none		0.612	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
AGAP6	414189	hgsc.bcm.edu	37	10	51769058	51769058	+	Silent	SNP	G	G	A	rs200123722	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:51769058G>A	ENST00000374056.4	+	7	1502	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	AGAP6_ENST00000412531.3_Silent_p.P391P			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						AGCTCAACCCGCCCCCCTCTC	0.507																																					p.P391P		Atlas-SNP	.											AGAP6,NS,carcinoma,+1,1	AGAP6	53	1	0			c.G1173A						scavenged	.																																			SO:0001819	synonymous_variant	414189	exon8			CAACCCGCCCCCC		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.1104G>A	10.37:g.51769058G>A		156.0	0.0	0		112.0	40.0	0.357143	NM_001077665		Silent	SNP	ENST00000374056.4	37																																																																																				G|0.985;A|0.015	0.015	strong		0.507	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
WNT9B	7484	hgsc.bcm.edu	37	17	44953637	44953637	+	Silent	SNP	G	G	A	rs62071993	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44953637G>A	ENST00000290015.2	+	4	680	c.627G>A	c.(625-627)acG>acA	p.T209T	WNT9B_ENST00000393461.2_Silent_p.T209T	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	209					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			TCAGGACCACGTGTAAGTGCC	0.647													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		20087	0.0		0.006	False		,,,				2504	0.0				p.T209T		Atlas-SNP	.											.	WNT9B	37	.	0			c.G627A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	62.0	53.0	56.0		627	-3.8	1.0	17	dbSNP_129	56	47,8553	31.2+/-83.2	0,47,4253	no	coding-synonymous	WNT9B	NM_003396.1		0,55,6448	AA,AG,GG		0.5465,0.1816,0.4229		209/358	44953637	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	7484	exon4			GACCACGTGTAAG	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.627G>A	17.37:g.44953637G>A		106.0	0.0	0		120.0	60.0	0.5	NM_003396	Q6UXT4|Q96Q09	Silent	SNP	ENST00000290015.2	37	CCDS11506.1																																																																																			G|0.997;A|0.003	0.003	strong		0.647	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
USP42	84132	hgsc.bcm.edu	37	7	6194379	6194379	+	Missense_Mutation	SNP	G	G	C	rs112550268	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6194379G>C	ENST00000306177.5	+	15	3352	c.3194G>C	c.(3193-3195)aGg>aCg	p.R1065T		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1065	Arg-rich.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		TACCATGACAGGTACGCCCTG	0.701													G|||	24	0.00479233	0.0008	0.0058	5008	,	,		7456	0.0		0.0089	False		,,,				2504	0.0102				p.R1065T		Atlas-SNP	.											.	USP42	138	.	0			c.G3194C						PASS	.	G	THR/ARG	14,4044		0,14,2015	8.0	11.0	10.0		3194	4.2	0.9	7	dbSNP_132	10	151,8175		0,151,4012	yes	missense	USP42	NM_032172.2	71	0,165,6027	CC,CG,GG		1.8136,0.345,1.3324	possibly-damaging	1065/1317	6194379	165,12219	2029	4163	6192	SO:0001583	missense	84132	exon15			ATGACAGGTACGC	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.3194G>C	7.37:g.6194379G>C	ENSP00000301962:p.Arg1065Thr	28.0	0.0	0		28.0	20.0	0.714286	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	18	0.008241758241758242	5	0.01016260162601626	3	0.008287292817679558	4	0.006993006993006993	6	0.0079155672823219	G	17.60	3.430585	0.62844	0.00345	0.018136	ENSG00000106346	ENST00000306177;ENST00000426246	T;T	0.62232	0.04;0.04	5.04	4.15	0.48705	.	0.237454	0.34906	N	0.003597	T	0.41834	0.1176	L	0.29908	0.895	0.25471	N	0.987828	D;D;D	0.71674	0.998;0.993;0.988	P;P;P	0.57776	0.795;0.827;0.676	T	0.44436	-0.9328	10	0.45353	T	0.12	.	5.3662	0.16115	0.2043:0.0:0.7957:0.0	.	961;1065;1065	A4D2N7;Q9H9J4-2;Q9H9J4	.;.;UBP42_HUMAN	T	1065;911	ENSP00000301962:R1065T;ENSP00000408217:R911T	ENSP00000301962:R1065T	R	+	2	0	USP42	6160904	1.000000	0.71417	0.861000	0.33841	0.410000	0.31052	3.170000	0.50816	2.728000	0.93425	0.655000	0.94253	AGG	G|0.992;C|0.008	0.008	strong		0.701	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
METTL25	84190	hgsc.bcm.edu	37	12	82780676	82780676	+	Silent	SNP	A	A	G	rs56337649	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:82780676A>G	ENST00000248306.3	+	2	423	c.354A>G	c.(352-354)caA>caG	p.Q118Q	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	118							methyltransferase activity (GO:0008168)										ATTCTGTACAAAACTTGGGAA	0.383													A|||	75	0.014976	0.0068	0.0288	5008	,	,		15133	0.0		0.0417	False		,,,				2504	0.0041				p.Q118Q		Atlas-SNP	.											.	.	.	.	0			c.A354G						PASS	.	A		60,4346	58.7+/-95.3	0,60,2143	136.0	136.0	136.0		354	2.4	1.0	12	dbSNP_129	136	370,8230	122.5+/-181.5	6,358,3936	no	coding-synonymous	C12orf26	NM_032230.2		6,418,6079	GG,GA,AA		4.3023,1.3618,3.3062		118/604	82780676	430,12576	2203	4300	6503	SO:0001819	synonymous_variant	84190	exon2			TGTACAAAACTTG	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.354A>G	12.37:g.82780676A>G		69.0	0.0	0		89.0	52.0	0.58427	NM_032230	Q9H5Y3	Silent	SNP	ENST00000248306.3	37	CCDS9024.1	47	0.02152014652014652	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	33	0.04353562005277045	A	2.978	-0.211051	0.06140	0.013618	0.043023	ENSG00000127720	ENST00000550058	.	.	.	6.14	2.44	0.29823	.	.	.	.	.	T	0.24928	0.0605	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15607	-1.0431	4	.	.	.	-3.6786	7.9708	0.30126	0.7528:0.0:0.2472:0.0	rs56337649	.	.	.	R	77	.	.	K	+	2	0	C12orf26	81304807	1.000000	0.71417	0.988000	0.46212	0.327000	0.28475	1.215000	0.32431	0.179000	0.19938	0.529000	0.55759	AAA	A|0.969;G|0.031	0.031	strong		0.383	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
C1orf210	149466	hgsc.bcm.edu	37	1	43748923	43748923	+	Splice_Site	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43748923T>G	ENST00000523677.1	-	2	252	c.19A>C	c.(19-21)Aca>Cca	p.T7P	C1orf210_ENST00000423420.1_Splice_Site_p.T7P	NM_001164829.1|NM_182517.2	NP_001158301.1|NP_872323.1	Q8IVY1	CA210_HUMAN	chromosome 1 open reading frame 210	7						integral component of membrane (GO:0016021)				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGTCACTCACTTTTGTTTGTC	0.587																																					p.T7P		Atlas-SNP	.											.	C1orf210	9	.	0			c.A19C						PASS	.						87.0	85.0	86.0					1																	43748923		2203	4300	6503	SO:0001630	splice_region_variant	149466	exon2			ACTCACTTTTGTT	BC041633	CCDS481.1	1p34.2	2006-03-22			ENSG00000253313	ENSG00000253313			28755	protein-coding gene	gene with protein product						12477932	Standard	NM_182517		Approved	MGC52423	uc001cit.4	Q8IVY1	OTTHUMG00000007289	ENST00000523677.1:c.19+1A>C	1.37:g.43748923T>G		350.0	0.0	0		392.0	16.0	0.0408163	NM_182517	D3DPX2	Missense_Mutation	SNP	ENST00000523677.1	37	CCDS481.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.311803	0.23821	.	.	ENSG00000253313	ENST00000523677;ENST00000423420	T;T	0.50001	0.76;0.76	3.99	3.99	0.46301	.	0.985827	0.08284	N	0.969437	T	0.65196	0.2668	M	0.63428	1.95	0.25968	N	0.982537	D	0.76494	0.999	D	0.83275	0.996	T	0.50381	-0.8835	9	.	.	.	.	9.554	0.39328	0.0:0.0:0.0:1.0	.	7	Q8IVY1	CA210_HUMAN	P	7	ENSP00000430918:T7P;ENSP00000429399:T7P	.	T	-	1	0	C1orf210	43521510	0.996000	0.38824	0.298000	0.25002	0.223000	0.24884	3.457000	0.53007	2.038000	0.60285	0.459000	0.35465	ACA	.	.	none		0.587	C1orf210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019035.2	NM_182517	Missense_Mutation
ITGB2	3689	hgsc.bcm.edu	37	21	46330667	46330667	+	Silent	SNP	G	G	A	rs5030667	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46330667G>A	ENST00000397850.2	-	3	483	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	ITGB2_ENST00000397852.1_Silent_p.L11L|ITGB2_ENST00000355153.4_Silent_p.L11L|ITGB2_ENST00000397854.3_Silent_p.L11L|ITGB2_ENST00000397857.1_Silent_p.L11L|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000302347.5_Silent_p.L11L|ITGB2_ENST00000397846.3_Silent_p.L11L			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	11					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGCCCCACCAGGGCGAGCAGT	0.657													G|||	71	0.0141773	0.0189	0.0144	5008	,	,		19347	0.0		0.0278	False		,,,				2504	0.0082				p.L11L		Atlas-SNP	.											.	ITGB2	107	.	0			c.C31T						PASS	.	G	,	67,4339	61.1+/-98.1	1,65,2137	39.0	43.0	42.0		31,31	2.9	0.2	21	dbSNP_113	42	257,8343	97.7+/-159.3	5,247,4048	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	6,312,6185	AA,AG,GG		2.9884,1.5207,2.4912	,	11/770,11/770	46330667	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon2			CCACCAGGGCGAG	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.31C>T	21.37:g.46330667G>A		80.0	0.0	0		74.0	28.0	0.378378	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			G|0.975;A|0.025	0.025	strong		0.657	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
PIGG	54872	hgsc.bcm.edu	37	4	509850	509850	+	Silent	SNP	T	T	C	rs11726338	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:509850T>C	ENST00000453061.2	+	6	1096	c.990T>C	c.(988-990)agT>agC	p.S330S	PIGG_ENST00000536264.1_Silent_p.S208S|PIGG_ENST00000504346.1_Silent_p.S241S|PIGG_ENST00000310340.5_Silent_p.S330S|PIGG_ENST00000509768.1_Silent_p.S241S|PIGG_ENST00000503111.1_Silent_p.S241S|PIGG_ENST00000296306.7_Silent_p.S241S|PIGG_ENST00000383028.4_Silent_p.S197S	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	330					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CAAAAGACAGTGTAGGGAGCC	0.463													C|||	103	0.0205671	0.0363	0.0187	5008	,	,		20071	0.0		0.0288	False		,,,				2504	0.0133				p.S330S		Atlas-SNP	.											.	PIGG	86	.	0			c.T990C						PASS	.	C	,	122,4284	815.1+/-416.2	3,116,2084	125.0	122.0	123.0		990,990	-6.1	0.0	4	dbSNP_120	123	232,8368	809.0+/-407.2	7,218,4075	no	coding-synonymous,coding-synonymous	PIGG	NM_001127178.1,NM_017733.3	,	10,334,6159	CC,CT,TT		2.6977,2.769,2.7218	,	330/984,330/976	509850	354,12652	2203	4300	6503	SO:0001819	synonymous_variant	54872	exon6			AGACAGTGTAGGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.990T>C	4.37:g.509850T>C		86.0	0.0	0		80.0	27.0	0.3375	NM_017733	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	37	CCDS46992.1																																																																																			T|0.972;C|0.028	0.028	strong		0.463	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
EPPK1	83481	hgsc.bcm.edu	37	8	144945535	144945535	+	Silent	SNP	G	G	A	rs73715515	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144945535G>A	ENST00000525985.1	-	2	1958	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A				P58107	EPIPL_HUMAN	epiplakin 1	629						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTTGCATCGGGCCTCATAGA	0.637													G|||	154	0.0307508	0.1097	0.0101	5008	,	,		18770	0.0		0.002	False		,,,				2504	0.0				p.A629A		Atlas-SNP	.											.	EPPK1	199	.	0			c.C1887T						PASS	.	G		306,3848		12,282,1783	28.0	30.0	29.0		1887	-1.8	0.0	8	dbSNP_130	29	12,8424		0,12,4206	no	coding-synonymous	EPPK1	NM_031308.1		12,294,5989	AA,AG,GG		0.1422,7.3664,2.5258		629/2420	144945535	318,12272	2077	4218	6295	SO:0001819	synonymous_variant	83481	exon1			GCATCGGGCCTCA	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.1887C>T	8.37:g.144945535G>A		62.0	0.0	0		60.0	22.0	0.366667	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.977;A|0.023	0.023	strong		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465449	39465449	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39465449G>A	ENST00000391352.1	-	1	56	c.57C>T	c.(55-57)tgC>tgT	p.C19C		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	19						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CCTCAGTGGAGCAGAGAGAGG	0.582																																					p.C19C		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C57T						PASS	.																																			SO:0001819	synonymous_variant	100505753	exon1			AGTGGAGCAGAGA	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.57C>T	17.37:g.39465449G>A		91.0	0.0	0		71.0	18.0	0.253521	NM_001146182		Silent	SNP	ENST00000391352.1	37	CCDS56032.1																																																																																			.	.	none		0.582	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
CYP2S1	29785	hgsc.bcm.edu	37	19	41703793	41703793	+	Silent	SNP	G	G	A	rs57266494	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41703793G>A	ENST00000310054.4	+	3	669	c.453G>A	c.(451-453)gcG>gcA	p.A151A	CYP2S1_ENST00000542619.1_Intron	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	151					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						TGATCCAGGCGGAGGCCCGGT	0.622													g|||	45	0.00898562	0.0015	0.0144	5008	,	,		15828	0.0		0.0288	False		,,,				2504	0.0041				p.A151A		Atlas-SNP	.											.	CYP2S1	47	.	0			c.G453A						PASS	.	G		44,4362	46.7+/-81.2	1,42,2160	57.0	56.0	56.0		453	-9.7	0.2	19	dbSNP_129	56	368,8232	121.7+/-180.7	6,356,3938	no	coding-synonymous	CYP2S1	NM_030622.6		7,398,6098	AA,AG,GG		4.2791,0.9986,3.1678		151/505	41703793	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	29785	exon3			CCAGGCGGAGGCC	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"""Cytochrome P450s"""	15654	protein-coding gene	gene with protein product		611529	"""cytochrome P450, subfamily IIS, polypeptide 1"""			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.453G>A	19.37:g.41703793G>A		46.0	0.0	0		52.0	22.0	0.423077	NM_030622	Q9BZ66	Silent	SNP	ENST00000310054.4	37	CCDS12573.1																																																																																			G|0.975;A|0.025	0.025	strong		0.622	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1		
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	G	rs186450029		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495725C>G	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.A16P|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000367858.5_Splice_Site	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCATGAAAGCTGTGGATGAA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.77-1G>C						PASS	.						73.0	73.0	73.0					6																	134495725		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon3			TGAAAGCTGTGGA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.77-1G>C	6.37:g.134495725C>G		67.0	0.0	0	1611	41.0	11.0	0.268293	NM_005627	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	37	CCDS5170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.8|27.8	4.862399|4.862399	0.91511|0.91511	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000528577;ENST00000475719;ENST00000461976|ENST00000367857	.|T	.|0.30981	.|1.51	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|.	.|.	.|.	.|.	.|T	.|0.30355	.|0.0762	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|P	.|0.52170	.|0.951	.|P	.|0.47827	.|0.558	.|T	.|0.01027	.|-1.1476	.|7	.|.	.|.	.|.	.|.	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|16	.|O00141-4	.|.	.|P	-1|16	.|ENSP00000356831:A16P	.|.	.|A	-|-	.|1	.|0	SGK1|SGK1	134537418|134537418	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	7.818000|7.818000	0.86416|0.86416	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	.|GCT	C|1.000;T|0.000	.	alt		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Intron
SAPCD2	89958	hgsc.bcm.edu	37	9	139959231	139959231	+	Silent	SNP	G	G	A	rs140919217	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139959231G>A	ENST00000409687.3	-	6	1192	c.1065C>T	c.(1063-1065)acC>acT	p.T355T	RP11-229P13.22_ENST00000435463.2_RNA|RP11-229P13.23_ENST00000456356.2_RNA	NM_178448.3	NP_848543.2	Q86UD0	SAPC2_HUMAN	suppressor APC domain containing 2	355						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)											CACTCTTCTCGGTCACCTCCT	0.677											OREG0019628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	15	0.00299521	0.0023	0.0043	5008	,	,		15193	0.0		0.008	False		,,,				2504	0.001				p.T355T		Atlas-SNP	.											.	.	.	.	0			c.C1065T						PASS	.	G		9,4377		0,9,2184	40.0	36.0	37.0		1065	-7.7	0.6	9	dbSNP_134	37	59,8523		0,59,4232	no	coding-synonymous	C9orf140	NM_178448.3		0,68,6416	AA,AG,GG		0.6875,0.2052,0.5244		355/395	139959231	68,12900	2193	4291	6484	SO:0001819	synonymous_variant	89958	exon6			CTTCTCGGTCACC	BC024299	CCDS7027.2	9q34.3	2012-02-08	2012-02-08	2012-02-08	ENSG00000186193	ENSG00000186193			28055	protein-coding gene	gene with protein product		612057	"""chromosome 9 open reading frame 140"""	C9orf140		12477932	Standard	NM_178448		Approved	p42.3	uc011men.2	Q86UD0	OTTHUMG00000020961	ENST00000409687.3:c.1065C>T	9.37:g.139959231G>A		114.0	0.0	0	1652	112.0	59.0	0.526786	NM_178448		Silent	SNP	ENST00000409687.3	37	CCDS7027.2																																																																																			G|0.995;A|0.005	0.005	strong		0.677	SAPCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055215.2	NM_178448	
DMBT1	1755	hgsc.bcm.edu	37	10	124345721	124345721	+	Silent	SNP	G	G	T	rs539603965		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124345721G>T	ENST00000338354.3	+	16	1711	c.1605G>T	c.(1603-1605)ctG>ctT	p.L535L	DMBT1_ENST00000368909.3_Silent_p.L535L|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Silent_p.L525L|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Silent_p.L525L			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	535	SRCR 4. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GCAGGCAGCTGGGCTGTGGCT	0.617																																					p.L535L	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G1605T						PASS	.						238.0	184.0	202.0					10																	124345721		2038	4168	6206	SO:0001819	synonymous_variant	1755	exon16			GCAGCTGGGCTGT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.1605G>T	10.37:g.124345721G>T		76.0	0.0	0		93.0	49.0	0.526882	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
ARRDC2	27106	hgsc.bcm.edu	37	19	18121454	18121454	+	Silent	SNP	G	G	C	rs147293119	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:18121454G>C	ENST00000222250.4	+	7	1229	c.1086G>C	c.(1084-1086)ccG>ccC	p.P362P	ARRDC2_ENST00000379656.3_Silent_p.P357P	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	362					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						TCCCGCTTCCGCAGGACCCCG	0.637													G|||	9	0.00179712	0.0	0.0029	5008	,	,		17520	0.0		0.007	False		,,,				2504	0.0				p.P362P		Atlas-SNP	.											.	ARRDC2	60	.	0			c.G1086C						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	63.0	62.0	63.0		1071,1086	-6.8	0.0	19	dbSNP_134	63	28,8572	20.4+/-63.3	0,28,4272	no	coding-synonymous,coding-synonymous	ARRDC2	NM_001025604.1,NM_015683.1	,	0,30,6473	CC,CG,GG		0.3256,0.0454,0.2307	,	357/403,362/408	18121454	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	27106	exon7			GCTTCCGCAGGAC		CCDS12370.1, CCDS32956.1	19p13.12	2008-02-05				ENSG00000105643			25225	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015683		Approved	CLONE24945, PP2703	uc002nhv.3	Q8TBH0		ENST00000222250.4:c.1086G>C	19.37:g.18121454G>C		34.0	0.0	0		48.0	25.0	0.520833	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Silent	SNP	ENST00000222250.4	37	CCDS12370.1																																																																																			G|0.998;C|0.002	0.002	strong		0.637	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683	
TTLL3	26140	hgsc.bcm.edu	37	3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	rs115917139	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9874914C>T	ENST00000547186.1	+	11	1897	c.1681C>T	c.(1681-1683)Cga>Tga	p.R561*	TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|TTLL3_ENST00000383827.1_Intron|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*|ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000397241.1_Intron	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	561					axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GCTGACCCAGCGAGGCTCTGG	0.647													C|||	115	0.0229633	0.0	0.0231	5008	,	,		16546	0.001		0.0408	False		,,,				2504	0.0583				p.R704X		Atlas-SNP	.											.	TTLL3	51	.	0			c.C2110T						PASS	.	C	stop/ARG,	28,3784		0,28,1878	29.0	31.0	30.0		2110,	3.6	0.3	3	dbSNP_132	30	360,7860		10,340,3760	yes	stop-gained,intron	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	10,368,5638	TT,TC,CC		4.3796,0.7345,3.2247	,	704/916,	9874914	388,11644	1906	4110	6016	SO:0001587	stop_gained	26140	exon11			ACCCAGCGAGGCT		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1681C>T	3.37:g.9874914C>T	ENSP00000446659:p.Arg561*	82.0	0.0	0		61.0	37.0	0.606557	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Nonsense_Mutation	SNP	ENST00000547186.1	37		43	0.019688644688644688	0	0.0	11	0.03038674033149171	0	0.0	32	0.04221635883905013	C	38	6.974468	0.97975	0.007345	0.043796	ENSG00000214021	ENST00000426895;ENST00000547186;ENST00000443148;ENST00000430793	.	.	.	5.39	3.58	0.41010	.	0.000000	0.27782	U	0.017874	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6056	0.33771	0.3092:0.5413:0.1495:0.0	rs3208837;rs17407417	.	.	.	X	704;561;499;349	.	ENSP00000392549:R704X	R	+	1	2	TTLL3	9849914	0.009000	0.17119	0.270000	0.24601	0.659000	0.38960	0.677000	0.25262	0.639000	0.30564	-0.152000	0.13540	CGA	C|0.975;T|0.025	0.025	strong		0.647	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
HCN1	348980	hgsc.bcm.edu	37	5	45396654	45396654	+	Silent	SNP	G	G	A	rs369683016		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:45396654G>A	ENST00000303230.4	-	4	1227	c.1170C>T	c.(1168-1170)gtC>gtT	p.V390V		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	390					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TGGCATGGCCGACAAACATGG	0.498																																					p.V390V		Atlas-SNP	.											.	HCN1	298	.	0			c.C1170T						PASS	.	A		0,4406		0,0,2203	78.0	68.0	72.0		1170	-10.8	0.0	5		72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HCN1	NM_021072.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		390/891	45396654	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	348980	exon4			ATGGCCGACAAAC	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1170C>T	5.37:g.45396654G>A		157.0	0.0	0		157.0	43.0	0.273885	NM_021072		Silent	SNP	ENST00000303230.4	37	CCDS3952.1																																																																																			.	.	weak		0.498	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
KCNC4	3749	hgsc.bcm.edu	37	1	110766185	110766185	+	Silent	SNP	C	C	T	rs368399763		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:110766185C>T	ENST00000369787.3	+	2	1305	c.1278C>T	c.(1276-1278)ggC>ggT	p.G426G	KCNC4_ENST00000438661.2_Silent_p.G426G|KCNC4_ENST00000413138.3_Silent_p.G426G|KCNC4_ENST00000412512.2_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	426					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCCCCATTGGCTTCTGGTGGG	0.587																																					p.G426G		Atlas-SNP	.											.	KCNC4	113	.	0			c.C1278T						PASS	.	C	,	0,4406		0,0,2203	117.0	106.0	110.0		1278,1278	3.8	1.0	1		110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	KCNC4	NM_001039574.2,NM_004978.4	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	426/627,426/636	110766185	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3749	exon2			CATTGGCTTCTGG	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6236	protein-coding gene	gene with protein product		176265	"""chromosome 1 open reading frame 30"""	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.1278C>T	1.37:g.110766185C>T		110.0	0.0	0		81.0	42.0	0.518519	NM_001039574	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	37	CCDS821.1																																																																																			.	.	none		0.587	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574	
PABPC3	5042	hgsc.bcm.edu	37	13	25670627	25670627	+	Silent	SNP	A	A	G	rs369126872		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25670627A>G	ENST00000281589.3	+	1	328	c.291A>G	c.(289-291)ggA>ggG	p.G97G		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	97					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GAAAAAGTGGAGTGGGCAACA	0.418																																					p.G97G		Atlas-SNP	.											.	PABPC3	129	.	0			c.A291G						PASS	.						96.0	89.0	92.0					13																	25670627		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			AAGTGGAGTGGGC	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.291A>G	13.37:g.25670627A>G		137.0	0.0	0		151.0	85.0	0.562914	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			.	.	alt		0.418	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
DGKQ	1609	hgsc.bcm.edu	37	4	956309	956309	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:956309C>T	ENST00000273814.3	-	18	2201	c.2128G>A	c.(2128-2130)Gtg>Atg	p.V710M	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	710	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TCCATGAGCACGGCGTCGGCC	0.672																																					p.V710M	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.G2128A						PASS	.						49.0	50.0	50.0					4																	956309		2200	4299	6499	SO:0001583	missense	1609	exon18			TGAGCACGGCGTC	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.2128G>A	4.37:g.956309C>T	ENSP00000273814:p.Val710Met	72.0	0.0	0		57.0	6.0	0.105263	NM_001347	Q6P3W4	Missense_Mutation	SNP	ENST00000273814.3	37	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520695	0.85495	.	.	ENSG00000145214	ENST00000273814	T	0.46451	0.87	4.8	4.8	0.61643	Diacylglycerol kinase, catalytic domain (3);	0.116434	0.56097	D	0.000022	T	0.62122	0.2402	M	0.62266	1.93	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.976;0.999	T	0.65969	-0.6039	10	0.87932	D	0	.	15.6931	0.77469	0.0:1.0:0.0:0.0	.	710;710	E9KL49;P52824	.;DGKQ_HUMAN	M	710	ENSP00000273814:V710M	ENSP00000273814:V710M	V	-	1	0	DGKQ	946309	0.963000	0.33076	0.945000	0.38365	0.517000	0.34286	2.895000	0.48648	2.338000	0.79540	0.655000	0.94253	GTG	.	.	none		0.672	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
CCDC168	643677	hgsc.bcm.edu	37	13	103388764	103388764	+	Silent	SNP	T	T	C	rs113711522	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103388764T>C	ENST00000322527.2	-	1	395	c.396A>G	c.(394-396)gtA>gtG	p.V132V		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	132																	ATACTGTTTGTACTCTGTCTT	0.473													T|||	12	0.00239617	0.0	0.0014	5008	,	,		22840	0.0		0.0099	False		,,,				2504	0.001				p.V4761V		Atlas-SNP	.											.	.	.	.	0			c.A14283G						PASS	.	T		1,1383		0,1,691	214.0	166.0	181.0		14283	0.3	0.0	13	dbSNP_132	181	50,3132		0,50,1541	no	coding-synonymous	CCDC168	NM_001146197.1		0,51,2232	CC,CT,TT		1.5713,0.0723,1.117		4761/7082	103388764	51,4515	692	1591	2283	SO:0001819	synonymous_variant	643677	exon4			TGTTTGTACTCTG		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.396A>G	13.37:g.103388764T>C		385.0	0.0	0		290.0	206.0	0.710345	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				T|0.996;C|0.004	0.004	strong		0.473	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
IRF1	3659	hgsc.bcm.edu	37	5	131825088	131825088	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131825088T>G	ENST00000245414.4	-	2	341	c.83A>C	c.(82-84)aAt>aCt	p.N28T	IRF1_ENST00000463784.1_Intron|IRF1_ENST00000405885.2_Missense_Mutation_p.N28T	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	28					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		ACTCACTTTATTAATCCAGAT	0.463																																					p.N28T		Atlas-SNP	.											.	IRF1	26	.	0			c.A83C						PASS	.						86.0	88.0	87.0					5																	131825088		2203	4300	6503	SO:0001583	missense	3659	exon2			ACTTTATTAATCC		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"""interferon regulatory factor-1"""	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.83A>C	5.37:g.131825088T>G	ENSP00000245414:p.Asn28Thr	69.0	0.0	0		48.0	19.0	0.395833	NM_002198	Q96GG7	Missense_Mutation	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943292	0.92593	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	D;D;D;D	0.98264	-4.83;-4.83;-4.83;-4.83	5.59	5.59	0.84812	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (3);	0.081526	0.85682	D	0.000000	D	0.98918	0.9633	M	0.83223	2.63	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.77557	0.99;0.953	D	0.99840	1.1061	10	0.87932	D	0	-31.594	16.0664	0.80878	0.0:0.0:0.0:1.0	.	28;28	Q5FBX3;P10914	.;IRF1_HUMAN	T	28	ENSP00000245414:N28T;ENSP00000384406:N28T;ENSP00000405655:N28T;ENSP00000396318:N28T	ENSP00000245414:N28T	N	-	2	0	IRF1	131852987	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.905000	0.87416	2.254000	0.74563	0.459000	0.35465	AAT	.	.	none		0.463	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	
MUC5B	727897	hgsc.bcm.edu	37	11	1281932	1281932	+	Silent	SNP	C	C	T	rs61734215	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1281932C>T	ENST00000529681.1	+	48	17101	c.17043C>T	c.(17041-17043)tgC>tgT	p.C5681C	MUC5B_ENST00000447027.1_Silent_p.C5684C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5681	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TCACCTTCTGCGAGGGCTCCT	0.652													C|||	19	0.00379393	0.0	0.0072	5008	,	,		18404	0.0		0.0119	False		,,,				2504	0.002				p.C5681C		Atlas-SNP	.											.	MUC5B	473	.	0			c.C17043T						PASS	.	C		13,4251		0,13,2119	50.0	56.0	54.0		17043	-2.0	1.0	11	dbSNP_129	54	80,8370		0,80,4145	no	coding-synonymous	MUC5B	NM_002458.2		0,93,6264	TT,TC,CC		0.9467,0.3049,0.7315		5681/5763	1281932	93,12621	2132	4225	6357	SO:0001819	synonymous_variant	727897	exon48			CTTCTGCGAGGGC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.17043C>T	11.37:g.1281932C>T		137.0	0.0	0		106.0	49.0	0.462264	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.992;T|0.008	0.008	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MTRR	4552	hgsc.bcm.edu	37	5	7873566	7873566	+	Silent	SNP	C	C	G	rs41282641	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:7873566C>G	ENST00000264668.2	+	3	321	c.291C>G	c.(289-291)cgC>cgG	p.R97R	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000341013.6_Intron|MTRR_ENST00000440940.2_Silent_p.R70R	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	97	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ACACAGCCCGCAAGTTTGTTA	0.468													C|||	4	0.000798722	0.0	0.0	5008	,	,		15728	0.0		0.003	False		,,,				2504	0.001				p.R97R		Atlas-SNP	.											.	MTRR	74	.	0			c.C291G						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	148.0	154.0	152.0		210,291	1.5	1.0	5	dbSNP_127	152	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	0,56,6447	GG,GC,CC		0.6395,0.0227,0.4306	,	70/699,97/726	7873566	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon3			AGCCCGCAAGTTT	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.291C>G	5.37:g.7873566C>G		94.0	0.0	0		80.0	37.0	0.4625	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.997;G|0.003	0.003	strong		0.468	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
PROKR1	10887	hgsc.bcm.edu	37	2	68882661	68882661	+	Missense_Mutation	SNP	A	A	G	rs34715748	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68882661A>G	ENST00000303786.3	+	3	1555	c.1135A>G	c.(1135-1137)Att>Gtt	p.I379V	PROKR1_ENST00000394342.2_Missense_Mutation_p.I379V			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	379					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.I379V(1)		endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCTCAAGACAATTGGGATGCC	0.488													A|||	234	0.0467252	0.0038	0.036	5008	,	,		21534	0.1111		0.0388	False		,,,				2504	0.0542				p.I379V		Atlas-SNP	.											PROKR1,NS,carcinoma,0,1	PROKR1	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1135G						PASS	.	A	VAL/ILE	36,4370	40.0+/-72.8	0,36,2167	66.0	62.0	63.0		1135	1.9	0.0	2	dbSNP_126	63	401,8199	128.3+/-186.6	10,381,3909	yes	missense	PROKR1	NM_138964.2	29	10,417,6076	GG,GA,AA		4.6628,0.8171,3.36	benign	379/394	68882661	437,12569	2203	4300	6503	SO:0001583	missense	10887	exon2			AAGACAATTGGGA	AF506287	CCDS1889.1	2p14	2012-08-08	2006-02-15	2006-02-15	ENSG00000169618	ENSG00000169618		"""GPCR / Class A : Prokineticin receptors"""	4524	protein-coding gene	gene with protein product		607122	"""G protein-coupled receptor 73"""	GPR73		10760605	Standard	NM_138964		Approved	PKR1, ZAQ, GPR73a	uc010yqj.2	Q8TCW9	OTTHUMG00000129567	ENST00000303786.3:c.1135A>G	2.37:g.68882661A>G	ENSP00000303775:p.Ile379Val	79.0	0.0	0		41.0	25.0	0.609756	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	103	0.04716117216117216	2	0.0040650406504065045	10	0.027624309392265192	55	0.09615384615384616	36	0.047493403693931395	A	1.463	-0.562016	0.03939	0.008171	0.046628	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.70869	-0.52;-0.52	4.22	1.88	0.25563	.	0.587506	0.18660	N	0.134753	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01652	-1.1303	10	0.32370	T	0.25	.	7.1531	0.25622	0.8081:0.0:0.1919:0.0	rs34715748;rs61732947	379	Q8TCW9	PKR1_HUMAN	V	379	ENSP00000303775:I379V;ENSP00000377874:I379V	ENSP00000303775:I379V	I	+	1	0	PROKR1	68736165	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	1.677000	0.37576	0.426000	0.26116	0.533000	0.62120	ATT	A|0.960;G|0.040	0.040	strong		0.488	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
LTB	4050	hgsc.bcm.edu	37	6	31549599	31549599	+	Missense_Mutation	SNP	T	T	C	rs532757438		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31549599T>C	ENST00000429299.2	-	2	207	c.200A>G	c.(199-201)cAa>cGa	p.Q67R	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	67				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						ACCCAGTCCTTGCTGGGCCTG	0.622																																					p.Q67R		Atlas-SNP	.											.	LTB	19	.	0			c.A200G						PASS	.						92.0	102.0	98.0					6																	31549599		1510	2708	4218	SO:0001583	missense	4050	exon2			AGTCCTTGCTGGG	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.200A>G	6.37:g.31549599T>C	ENSP00000410481:p.Gln67Arg	70.0	0.0	0		84.0	46.0	0.547619	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	T	4.177	0.031512	0.08101	.	.	ENSG00000227507	ENST00000429299	T	0.20738	2.05	5.45	-0.106	0.13596	.	1.357640	0.04844	N	0.441054	T	0.05823	0.0152	M	0.64997	1.995	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.32561	-0.9902	10	0.16420	T	0.52	0.0039	1.252	0.01984	0.3122:0.0874:0.1618:0.4386	.	67	Q06643	TNFC_HUMAN	R	67	ENSP00000410481:Q67R	ENSP00000410481:Q67R	Q	-	2	0	LTB	31657578	0.024000	0.19004	0.068000	0.19968	0.859000	0.49053	0.201000	0.17276	0.044000	0.15775	0.533000	0.62120	CAA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
BTG1	694	hgsc.bcm.edu	37	12	92539223	92539223	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:92539223C>T	ENST00000256015.3	-	1	450	c.89G>A	c.(88-90)gGg>gAg	p.G30E	RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	30					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GCTCGTGAGCCCCTTGGTGCG	0.677			T	MYC	BCLL																																p.G30E		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.G89A						PASS	.						43.0	46.0	45.0					12																	92539223		2203	4300	6503	SO:0001583	missense	694	exon1			GTGAGCCCCTTGG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.89G>A	12.37:g.92539223C>T	ENSP00000256015:p.Gly30Glu	140.0	0.0	0		151.0	48.0	0.317881	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678759	0.68042	.	.	ENSG00000133639	ENST00000256015	T	0.22539	1.95	3.92	3.92	0.45320	Anti-proliferative protein (3);	0.111608	0.64402	D	0.000010	T	0.26122	0.0637	L	0.59436	1.845	0.80722	D	1	P	0.39920	0.695	B	0.39971	0.315	T	0.16305	-1.0407	10	0.59425	D	0.04	-11.2093	16.1014	0.81175	0.0:1.0:0.0:0.0	.	30	P62324	BTG1_HUMAN	E	30	ENSP00000256015:G30E	ENSP00000256015:G30E	G	-	2	0	BTG1	91063354	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.620000	0.74224	1.996000	0.58369	0.455000	0.32223	GGG	.	.	none		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
TLN1	7094	hgsc.bcm.edu	37	9	35733116	35733116	+	5'Flank	SNP	C	C	T	rs200166825		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35733116C>T	ENST00000314888.9	-	0	0				CREB3_ENST00000353704.2_Missense_Mutation_p.R85W|CREB3_ENST00000486056.1_3'UTR|TLN1_ENST00000540444.1_5'Flank	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTCCCTCCCACGGGAAACTGT	0.532																																					p.R85W		Atlas-SNP	.											.	CREB3	24	.	0			c.C253T						PASS	.		TRP/ARG	0,4406		0,0,2203	103.0	100.0	101.0		253	4.8	0.2	9		101	3,8597	3.0+/-9.4	0,3,4297	no	missense	CREB3	NM_006368.4	101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	85/372	35733116	3,13003	2203	4300	6503	SO:0001631	upstream_gene_variant	10488	exon2			CTCCCACGGGAAA	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874		9.37:g.35733116C>T	Exception_encountered	263.0	0.0	0		250.0	135.0	0.54	NM_006368	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	c	16.81	3.226051	0.58668	0.0	3.49E-4	ENSG00000107175	ENST00000353704	T	0.64991	-0.13	4.77	4.77	0.60923	.	0.983520	0.08280	N	0.970123	T	0.49795	0.1578	N	0.14661	0.345	0.24140	N	0.995734	D	0.63880	0.993	B	0.43916	0.436	T	0.43278	-0.9401	10	0.87932	D	0	.	10.7772	0.46356	0.0:0.9013:0.0:0.0987	.	85	O43889-2	.	W	85	ENSP00000342136:R85W	ENSP00000342136:R85W	R	+	1	2	CREB3	35723116	0.403000	0.25319	0.245000	0.24217	0.122000	0.20287	1.449000	0.35123	2.381000	0.81170	0.580000	0.79431	CGG	C|0.999;T|0.001	0.001	weak		0.532	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
POM121L2	94026	hgsc.bcm.edu	37	6	27278838	27278838	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27278838T>G	ENST00000444565.1	-	1	1111	c.1112A>C	c.(1111-1113)aAc>aCc	p.N371T	POM121L2_ENST00000377451.2_Intron	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	371										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						AGGGTCTGTGTTGACCTCAGT	0.488																																					p.N371T		Atlas-SNP	.											.	POM121L2	61	.	0			c.A1112C						PASS	.						287.0	242.0	256.0					6																	27278838		692	1591	2283	SO:0001583	missense	94026	exon1			TCTGTGTTGACCT	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.1112A>C	6.37:g.27278838T>G	ENSP00000392726:p.Asn371Thr	157.0	0.0	0		135.0	32.0	0.237037	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	.	.	.	.	.	.	.	.	.	.	T	5.881	0.346626	0.11126	.	.	ENSG00000158553	ENST00000444565	T	0.12569	2.67	3.54	1.67	0.24075	.	.	.	.	.	T	0.04952	0.0133	L	0.52011	1.625	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.87932	D	0	.	8.2949	0.31980	0.0:0.0:0.5676:0.4324	.	371	C9J1I7	.	T	371	ENSP00000392726:N371T	ENSP00000392726:N371T	N	-	2	0	POM121L2	27386817	0.000000	0.05858	0.003000	0.11579	0.338000	0.28826	0.128000	0.15810	0.441000	0.26529	-0.233000	0.12211	AAC	.	.	none		0.488	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
JADE2	23338	hgsc.bcm.edu	37	5	133901934	133901934	+	Silent	SNP	C	C	T	rs148155246	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:133901934C>T	ENST00000402835.1	+	9	1353	c.1098C>T	c.(1096-1098)gaC>gaT	p.D366D	PHF15_ENST00000282605.4_Silent_p.D366D|PHF15_ENST00000361895.2_Silent_p.D366D|PHF15_ENST00000395003.1_Silent_p.D366D																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCACAGTGACGGGGGCCCAC	0.587													C|||	4	0.000798722	0.0	0.0	5008	,	,		20135	0.0		0.004	False		,,,				2504	0.0				p.D366D		Atlas-SNP	.											.	PHF15	60	.	0			c.C1098T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	93.0	83.0	86.0		1098	-11.1	0.0	5	dbSNP_134	86	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	PHF15	NM_015288.4		0,34,6469	TT,TC,CC		0.3721,0.0454,0.2614		366/791	133901934	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	23338	exon9			CAGTGACGGGGGC																												ENST00000402835.1:c.1098C>T	5.37:g.133901934C>T		114.0	0.0	0		84.0	43.0	0.511905	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																				C|0.997;T|0.003	0.003	strong		0.587	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
ISG20	3669	hgsc.bcm.edu	37	15	89182736	89182736	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89182736G>A	ENST00000306072.5	+	2	497	c.139G>A	c.(139-141)Gga>Aga	p.G47R	ISG20_ENST00000560741.1_Missense_Mutation_p.G47R|ISG20_ENST00000379224.5_Missense_Mutation_p.G47R	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	47					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			CCGGCCTGAGGGAGAGATCAC	0.642																																					p.G47R		Atlas-SNP	.											.	ISG20	17	.	0			c.G139A						PASS	.						68.0	68.0	68.0					15																	89182736		2200	4299	6499	SO:0001583	missense	3669	exon2			CCTGAGGGAGAGA	X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"""interferon stimulated gene (20kD)"""			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.139G>A	15.37:g.89182736G>A	ENSP00000306565:p.Gly47Arg	58.0	0.0	0		64.0	16.0	0.25	NM_002201	O00441|O00586	Missense_Mutation	SNP	ENST00000306072.5	37	CCDS10345.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365645	0.41902	.	.	ENSG00000172183	ENST00000306072;ENST00000379224	T;T	0.19938	2.11;2.11	4.81	3.9	0.45041	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	1.105290	0.06796	N	0.787879	T	0.19886	0.0478	L	0.56396	1.775	0.09310	N	1	P	0.34562	0.457	B	0.28011	0.085	T	0.27434	-1.0074	10	0.18276	T	0.48	-10.2487	7.7296	0.28779	0.1947:0.0:0.8053:0.0	.	47	Q96AZ6	ISG20_HUMAN	R	47	ENSP00000306565:G47R;ENSP00000368526:G47R	ENSP00000306565:G47R	G	+	1	0	ISG20	86983740	0.000000	0.05858	0.130000	0.21974	0.967000	0.64934	0.117000	0.15583	1.002000	0.39104	0.561000	0.74099	GGA	.	.	none		0.642	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201	
NRXN1	9378	hgsc.bcm.edu	37	2	51255307	51255307	+	Silent	SNP	G	G	T	rs55640811		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:51255307G>T	ENST00000406316.2	-	2	1581	c.105C>A	c.(103-105)ggC>ggA	p.G35G	NRXN1_ENST00000405581.1_Silent_p.G35G|NRXN1_ENST00000405472.3_Silent_p.G35G|NRXN1_ENST00000406859.3_Silent_p.G35G|NRXN1_ENST00000404971.1_Silent_p.G35G|NRXN1_ENST00000402717.3_Silent_p.G35G|NRXN1_ENST00000401669.2_Silent_p.G35G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	35	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GGCCCTCGGCGCCCGGAAACT	0.692																																					p.G35G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C105A						PASS	.	G	,	2,3844		0,2,1921	5.0	7.0	7.0		105,105	-1.0	1.0	2	dbSNP_129	7	8,8162		0,8,4077	no	coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4	,	0,10,5998	TT,TG,GG		0.0979,0.052,0.0832	,	35/1548,35/1478	51255307	10,12006	1923	4085	6008	SO:0001819	synonymous_variant	9378	exon2			CTCGGCGCCCGGA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.105C>A	2.37:g.51255307G>T		37.0	0.0	0		38.0	22.0	0.578947	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	weak		0.692	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
VASN	114990	hgsc.bcm.edu	37	16	4431373	4431373	+	Silent	SNP	G	G	C	rs740374	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4431373G>C	ENST00000304735.3	+	2	650	c.495G>C	c.(493-495)ccG>ccC	p.P165P	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	165				Missing (in Ref. 2; AAQ88665). {ECO:0000305}.	cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CACTGCCCCCGCTGCGCCTGC	0.697													G|||	66	0.0131789	0.0008	0.0202	5008	,	,		13608	0.0		0.0358	False		,,,				2504	0.0153				p.P165P		Atlas-SNP	.											.	VASN	21	.	0			c.G495C						PASS	.	G	,,,,	25,4267		0,25,2121	12.0	9.0	10.0		,,,,495	-11.6	0.0	16	dbSNP_86	10	191,8271		1,189,4041	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	1,214,6162	CC,CG,GG		2.2571,0.5825,1.6936	,,,,	,,,,165/674	4431373	216,12538	2146	4231	6377	SO:0001819	synonymous_variant	114990	exon2			GCCCCCGCTGCGC	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"""slit-like 2 (Drosophila)"""	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.495G>C	16.37:g.4431373G>C		27.0	0.0	0		24.0	15.0	0.625	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			G|0.986;C|0.014	0.014	strong		0.697	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440	
RTN3	10313	hgsc.bcm.edu	37	11	63487033	63487033	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63487033T>C	ENST00000377819.5	+	3	1213	c.1059T>C	c.(1057-1059)gaT>gaC	p.D353D	RTN3_ENST00000354497.4_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000339997.4_Silent_p.D334D|RTN3_ENST00000540798.1_Silent_p.D241D|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	353					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						AACAGACCGATAAATCTTCTG	0.383																																					p.D353D		Atlas-SNP	.											.	RTN3	104	.	0			c.T1059C						PASS	.						57.0	57.0	57.0					11																	63487033		2201	4298	6499	SO:0001819	synonymous_variant	10313	exon3			GACCGATAAATCT	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.1059T>C	11.37:g.63487033T>C		87.0	0.0	0		86.0	21.0	0.244186	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Silent	SNP	ENST00000377819.5	37	CCDS58141.1																																																																																			.	.	none		0.383	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054	
PBX1	5087	hgsc.bcm.edu	37	1	164761924	164761924	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:164761924A>C	ENST00000420696.2	+	3	647	c.459A>C	c.(457-459)aaA>aaC	p.K153N	PBX1_ENST00000560641.1_Missense_Mutation_p.K48N|PBX1_ENST00000367897.1_Missense_Mutation_p.K153N|PBX1_ENST00000401534.1_Missense_Mutation_p.K153N|PBX1_ENST00000540246.1_Missense_Mutation_p.K48N|PBX1_ENST00000559240.1_Missense_Mutation_p.K153N|PBX1_ENST00000540236.1_Missense_Mutation_p.K153N	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	153					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						ACAGAGCCAAACTCTCACAGA	0.592			T	"""TCF3, EWSR1"""	"""pre B-ALL, myoepithelioma"""																																p.K153N		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"""L, M"""	.	PBX1	60	.	0			c.A459C						PASS	.						32.0	38.0	36.0					1																	164761924		2202	4300	6502	SO:0001583	missense	5087	exon3			AGCCAAACTCTCA	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"""Homeoboxes / TALE class"""	8632	protein-coding gene	gene with protein product		176310	"""pre-B-cell leukemia transcription factor 1"""				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.459A>C	1.37:g.164761924A>C	ENSP00000405890:p.Lys153Asn	58.0	0.0	0		51.0	13.0	0.254902	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030748	0.75504	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13	5.23	1.65	0.23941	PBX (1);	0.000000	0.85682	D	0.000000	T	0.52821	0.1758	M	0.86651	2.83	0.09310	N	0.999999	D;D;D;D;D	0.71674	0.998;0.998;0.995;0.998;0.996	D;D;D;D;D	0.76575	0.982;0.982;0.962;0.988;0.978	T	0.59182	-0.7502	9	0.87932	D	0	-9.1405	8.5144	0.33237	0.6736:0.0:0.3264:0.0	.	48;153;153;153;153	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	N	153;153;153;153;153;48	ENSP00000341455:K153N;ENSP00000405890:K153N;ENSP00000356872:K153N;ENSP00000439943:K153N;ENSP00000384856:K153N;ENSP00000440869:K48N	ENSP00000341455:K153N	K	+	3	2	PBX1	163028548	0.981000	0.34729	1.000000	0.80357	0.998000	0.95712	0.288000	0.18939	0.297000	0.22615	0.460000	0.39030	AAA	.	.	none		0.592	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585	
HAVCR1	26762	hgsc.bcm.edu	37	5	156482296	156482296	+	Missense_Mutation	SNP	C	C	G	rs56084311	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156482296C>G	ENST00000339252.3	-	2	827	c.295G>C	c.(295-297)Gac>Cac	p.D99H	HAVCR1_ENST00000522693.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000425854.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000523175.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000544197.1_Missense_Mutation_p.D99H	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	Ig-like V-type.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACGCCACTGTCAGACACAGCT	0.458													C|||	17	0.00339457	0.0008	0.0029	5008	,	,		20324	0.0		0.0129	False		,,,				2504	0.001				p.D99H		Atlas-SNP	.											HAVCR1,NS,carcinoma,+1,1	HAVCR1	84	1	0			c.G295C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	9,4029		0,9,2010	93.0	82.0	85.0		295,295,295	5.8	1.0	5	dbSNP_129	85	97,8309		0,97,4106	yes	missense,missense,missense	HAVCR1	NM_001099414.1,NM_001173393.1,NM_012206.2	81,81,81	0,106,6116	GG,GC,CC		1.1539,0.2229,0.8518	probably-damaging,probably-damaging,probably-damaging	99/365,99/365,99/365	156482296	106,12338	2019	4203	6222	SO:0001583	missense	26762	exon3			CACTGTCAGACAC	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.295G>C	5.37:g.156482296C>G	ENSP00000344844:p.Asp99His	112.0	0.0	0		133.0	71.0	0.533835	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	CCDS43392.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	C	13.39	2.222182	0.39300	0.002229	0.011539	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92227	0.7535	H	0.94771	3.58	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93034	0.6451	10	0.87932	D	0	-45.3525	18.7919	0.91976	0.0:1.0:0.0:0.0	rs56084311	99;99	F1CME6;Q96D42	.;HAVR1_HUMAN	H	99	ENSP00000428524:D99H;ENSP00000427898:D99H;ENSP00000344844:D99H;ENSP00000403333:D99H;ENSP00000440258:D99H;ENSP00000428422:D99H	ENSP00000344844:D99H	D	-	1	0	HAVCR1	156414874	0.995000	0.38212	0.961000	0.40146	0.046000	0.14306	4.840000	0.62817	2.729000	0.93468	0.650000	0.86243	GAC	C|0.992;G|0.008	0.008	strong		0.458	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
NLRP5	126206	hgsc.bcm.edu	37	19	56549518	56549518	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56549518A>G	ENST00000390649.3	+	10	2743	c.2743A>G	c.(2743-2745)Agt>Ggt	p.S915G		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	915					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AATGCCTCTCAGTGATGCCTT	0.517																																					p.S915G		Atlas-SNP	.											.	NLRP5	217	.	0			c.A2743G						PASS	.						132.0	134.0	133.0					19																	56549518		2108	4229	6337	SO:0001583	missense	126206	exon10			CCTCTCAGTGATG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2743A>G	19.37:g.56549518A>G	ENSP00000375063:p.Ser915Gly	127.0	0.0	0		133.0	24.0	0.180451	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	A	4.665	0.123582	0.08931	.	.	ENSG00000171487	ENST00000390649	T	0.52526	0.66	3.59	1.27	0.21489	.	0.882081	0.09271	N	0.825144	T	0.26738	0.0654	N	0.13272	0.32	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.22068	-1.0227	10	0.29301	T	0.29	.	4.0597	0.09832	0.212:0.0:0.2079:0.5801	.	915	P59047	NALP5_HUMAN	G	915	ENSP00000375063:S915G	ENSP00000375063:S915G	S	+	1	0	NLRP5	61241330	0.956000	0.32656	0.012000	0.15200	0.003000	0.03518	0.996000	0.29719	0.045000	0.15804	-0.408000	0.06270	AGT	.	.	none		0.517	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
ITIH6	347365	hgsc.bcm.edu	37	X	54783779	54783779	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:54783779T>C	ENST00000218436.6	-	8	2757	c.2728A>G	c.(2728-2730)Agt>Ggt	p.S910G		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	910	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S910R(1)									CCTGTGGAACTTGAGATTGTA	0.557																																					p.S910G		Atlas-SNP	.											.	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2728G						PASS	.						100.0	89.0	93.0					X																	54783779		2203	4300	6503	SO:0001583	missense	347365	exon8			TGGAACTTGAGAT	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.2728A>G	X.37:g.54783779T>C	ENSP00000218436:p.Ser910Gly	55.0	0.0	0		94.0	7.0	0.0744681	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	T	6.767	0.510364	0.12883	.	.	ENSG00000102313	ENST00000218436	T	0.02656	4.21	3.38	0.712	0.18167	.	1.639110	0.04365	U	0.358064	T	0.02342	0.0072	N	0.19112	0.55	0.09310	N	1	B	0.30326	0.276	B	0.25759	0.063	T	0.43702	-0.9375	10	0.56958	D	0.05	.	3.6381	0.08157	0.2181:0.0:0.2212:0.5607	.	910	Q6UXX5	ITH5L_HUMAN	G	910	ENSP00000218436:S910G	ENSP00000218436:S910G	S	-	1	0	ITIH5L	54800504	0.004000	0.15560	0.001000	0.08648	0.081000	0.17604	0.363000	0.20301	-0.043000	0.13513	0.412000	0.27726	AGT	.	.	none		0.557	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
MAP3K1	4214	hgsc.bcm.edu	37	5	56178615	56178615	+	Silent	SNP	A	A	C	rs55912465	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:56178615A>C	ENST00000399503.3	+	14	3588	c.3588A>C	c.(3586-3588)tcA>tcC	p.S1196S		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1196					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGGCAATGTCAGCGTCTCAGG	0.393													A|||	3	0.000599042	0.0	0.0014	5008	,	,		22938	0.0		0.002	False		,,,				2504	0.0				p.S1196S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A3588C						PASS	.	A		3,4211		0,3,2104	83.0	85.0	84.0		3588	0.2	1.0	5	dbSNP_129	84	39,8457		0,39,4209	no	coding-synonymous	MAP3K1	NM_005921.1		0,42,6313	CC,CA,AA		0.459,0.0712,0.3304		1196/1513	56178615	42,12668	2107	4248	6355	SO:0001819	synonymous_variant	4214	exon14			AATGTCAGCGTCT	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3588A>C	5.37:g.56178615A>C		55.0	0.0	0		47.0	28.0	0.595745	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			A|0.993;C|0.007	0.007	strong		0.393	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
BTG2	7832	hgsc.bcm.edu	37	1	203274835	203274835	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274835G>A	ENST00000290551.4	+	1	172	c.101G>A	c.(100-102)aGg>aAg	p.R34K	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			AGCGAGCAGAGGCTTAAGGTC	0.711																																					p.R34K		Atlas-SNP	.											.	BTG2	16	.	0			c.G101A						PASS	.						15.0	16.0	16.0					1																	203274835		2146	4205	6351	SO:0001583	missense	7832	exon1			AGCAGAGGCTTAA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.101G>A	1.37:g.203274835G>A	ENSP00000290551:p.Arg34Lys	124.0	0.0	0		110.0	31.0	0.281818	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.239008	0.58995	.	.	ENSG00000159388	ENST00000290551	T	0.21543	2.0	4.66	2.79	0.32731	Anti-proliferative protein (3);	0.165673	0.37761	N	0.001941	T	0.11067	0.0270	N	0.13299	0.325	0.31292	N	0.689358	B	0.14012	0.009	B	0.20577	0.03	T	0.08066	-1.0740	10	0.41790	T	0.15	-8.3253	6.0943	0.20010	0.386:0.0:0.614:0.0	.	34	P78543	BTG2_HUMAN	K	34	ENSP00000290551:R34K	ENSP00000290551:R34K	R	+	2	0	BTG2	201541458	1.000000	0.71417	0.012000	0.15200	0.830000	0.47004	5.105000	0.64591	0.589000	0.29677	0.478000	0.44815	AGG	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
FAM65B	9750	hgsc.bcm.edu	37	6	24839461	24839461	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24839461T>G	ENST00000259698.4	-	15	2135	c.1960A>C	c.(1960-1962)Agt>Cgt	p.S654R	AL512428.1_ENST00000583229.1_RNA|FAM65B_ENST00000538035.1_Missense_Mutation_p.S633R|FAM65B_ENST00000473070.1_5'Flank	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	654					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						ACTGTGAGACTTAAACTGGAA	0.473																																					p.S654R		Atlas-SNP	.											.	FAM65B	134	.	0			c.A1960C						PASS	.						77.0	68.0	71.0					6																	24839461		692	1591	2283	SO:0001583	missense	9750	exon15			TGAGACTTAAACT	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1960A>C	6.37:g.24839461T>G	ENSP00000259698:p.Ser654Arg	120.0	0.0	0		118.0	38.0	0.322034	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931738	0.92389	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.50813	0.73;0.73	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.68526	-0.5385	10	0.72032	D	0.01	-20.4236	16.2879	0.82732	0.0:0.0:0.0:1.0	.	633;654	F5GX51;Q9Y4F9	.;FA65B_HUMAN	R	654;633	ENSP00000259698:S654R;ENSP00000441138:S633R	ENSP00000259698:S654R	S	-	1	0	FAM65B	24947440	1.000000	0.71417	0.970000	0.41538	0.998000	0.95712	7.353000	0.79414	2.242000	0.73789	0.533000	0.62120	AGT	.	.	none		0.473	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
SGK1	6446	hgsc.bcm.edu	37	6	134495155	134495155	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495155G>A	ENST00000237305.7	-	3	304	c.216C>T	c.(214-216)aaC>aaT	p.N72N	SGK1_ENST00000528577.1_Silent_p.N100N|SGK1_ENST00000413996.3_Silent_p.N86N|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Silent_p.N62N|SGK1_ENST00000475719.2_Silent_p.N72N|SGK1_ENST00000367858.5_Silent_p.N167N	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	72					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GAGGAGAAGGGTTGGCATTCA	0.443																																					p.N167N		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,5	SGK1	387	5	0			c.C501T						scavenged	.						151.0	146.0	148.0					6																	134495155		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon5			AGAAGGGTTGGCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.216C>T	6.37:g.134495155G>A		76.0	1.0	0.0131579		61.0	12.0	0.196721	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.443	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
UHRF2	115426	hgsc.bcm.edu	37	9	6413498	6413498	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413498T>A	ENST00000276893.5	+	1	176	c.8T>A	c.(7-9)aTa>aAa	p.I3K	UHRF2_ENST00000381373.3_Missense_Mutation_p.I3K|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	3	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		AAGATGTGGATACAGGTTCGC	0.662																																					p.I3K		Atlas-SNP	.											.	UHRF2	50	.	0			c.T8A						PASS	.						57.0	58.0	57.0					9																	6413498		2203	4300	6503	SO:0001583	missense	115426	exon1			TGTGGATACAGGT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.8T>A	9.37:g.6413498T>A	ENSP00000276893:p.Ile3Lys	73.0	0.0	0		70.0	13.0	0.185714	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	T	34	5.300914	0.95601	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.57907	0.37;0.37	4.87	4.87	0.63330	Ubiquitin supergroup (1);Ubiquitin (1);	0.000000	0.85682	D	0.000000	T	0.80544	0.4643	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.86923	0.2068	10	0.87932	D	0	-7.8255	14.2948	0.66304	0.0:0.0:0.0:1.0	.	3	Q96PU4	UHRF2_HUMAN	K	3	ENSP00000276893:I3K;ENSP00000370778:I3K	ENSP00000276893:I3K	I	+	2	0	UHRF2	6403498	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.099000	0.76981	2.043000	0.60533	0.459000	0.35465	ATA	.	.	none		0.662	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
OPA1	4976	hgsc.bcm.edu	37	3	193332566	193332566	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193332566A>G	ENST00000392438.3	+	2	321	c.87A>G	c.(85-87)ccA>ccG	p.P29P	OPA1_ENST00000361150.2_Silent_p.P29P|OPA1_ENST00000361510.2_Silent_p.P29P|OPA1_ENST00000361715.2_Silent_p.P29P|OPA1_ENST00000361908.3_Silent_p.P29P|OPA1_ENST00000361828.2_Silent_p.P29P	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	29					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		GAAGTTTACCACTACAAAAAC	0.388																																					p.P29P		Atlas-SNP	.											.	OPA1	79	.	0			c.A87G						PASS	.						119.0	109.0	112.0					3																	193332566		2203	4300	6503	SO:0001819	synonymous_variant	4976	exon2			TTTACCACTACAA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.87A>G	3.37:g.193332566A>G		155.0	0.0	0		158.0	8.0	0.0506329	NM_130832	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			.	.	none		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
SQSTM1	8878	hgsc.bcm.edu	37	5	179263542	179263542	+	Silent	SNP	C	C	T	rs374985304		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179263542C>T	ENST00000389805.4	+	8	1450	c.1272C>T	c.(1270-1272)atC>atT	p.I424I	SQSTM1_ENST00000360718.5_Silent_p.I340I|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S341L|SQSTM1_ENST00000376929.3_Silent_p.I340I|C5orf45_ENST00000523267.1_5'Flank|C5orf45_ENST00000403396.2_3'UTR|SQSTM1_ENST00000402874.3_Silent_p.I340I	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	424	Interaction with NTRK1. {ECO:0000250}.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.I424I(1)	SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACTATGACATCGGAGCGGCTC	0.572																																					p.I424I		Atlas-SNP	.											SQSTM1,NS,carcinoma,0,1	SQSTM1	30	1	1	Substitution - coding silent(1)	endometrium(1)	c.C1272T						PASS	.	C	,,	0,4406		0,0,2203	145.0	138.0	141.0		1020,1020,1272	-4.3	0.9	5		141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	340/357,340/357,424/441	179263542	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon8			TGACATCGGAGCG	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"""Paget disease of bone 3"", ""oxidative stress induced like"""	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.1272C>T	5.37:g.179263542C>T		81.0	0.0	0		70.0	30.0	0.428571	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	C	4.985	0.182894	0.09495	0.0	1.16E-4	ENSG00000161011	ENST00000510187	T	0.15372	2.43	4.53	-4.32	0.03688	.	.	.	.	.	T	0.14485	0.0350	.	.	.	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.04400	-1.0954	8	0.72032	D	0.01	-13.2762	13.8049	0.63225	0.0:0.3694:0.0:0.6306	.	341	E7EMC7	.	L	341	ENSP00000424477:S341L	ENSP00000424477:S341L	S	+	2	0	SQSTM1	179196148	0.000000	0.05858	0.912000	0.35992	0.106000	0.19336	-1.795000	0.01752	-1.138000	0.02884	-1.263000	0.01449	TCG	.	.	weak		0.572	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1		
MYO1C	4641	hgsc.bcm.edu	37	17	1382889	1382889	+	Silent	SNP	G	G	A	rs146685153		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1382889G>A	ENST00000575158.1	-	8	1088	c.912C>T	c.(910-912)acC>acT	p.T304T	MYO1C_ENST00000573198.1_5'UTR|MYO1C_ENST00000438665.2_Silent_p.T320T|MYO1C_ENST00000359786.5_Silent_p.T339T|MYO1C_ENST00000545534.2_Silent_p.T315T|MYO1C_ENST00000361007.2_Silent_p.T304T			Q12965	MYO1E_HUMAN	myosin IC	309	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CACTCACCCTGGTCAGATACT	0.662																																					p.T339T		Atlas-SNP	.											.	MYO1C	57	.	0			c.C1017T						PASS	.	G	,,	0,4406		0,0,2203	63.0	47.0	52.0		1017,960,912	2.9	1.0	17	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	339/1064,320/1045,304/1029	1382889	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon8			CACCCTGGTCAGA	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.912C>T	17.37:g.1382889G>A		138.0	0.0	0		123.0	57.0	0.463415	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			G|1.000;A|0.000	0.000	weak		0.662	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
PTPRQ	374462	hgsc.bcm.edu	37	12	80865948	80865948	+	Silent	SNP	A	A	G	rs61729291	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:80865948A>G	ENST00000266688.5	+	13	1092	c.1092A>G	c.(1090-1092)acA>acG	p.T364T				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	410	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CACCATTTACAATGTATGATG	0.398													A|||	115	0.0229633	0.0038	0.0548	5008	,	,		18585	0.0		0.0646	False		,,,				2504	0.0072				p.T196T		Atlas-SNP	.											.	PTPRQ	119	.	0			c.A588G						PASS	.	A		15,1369		0,15,677	108.0	89.0	94.0		650	-3.2	0.3	12	dbSNP_129	94	168,3014		5,158,1428	no	coding-synonymous	PTPRQ	NM_001145026.1		5,173,2105	GG,GA,AA		5.2797,1.0838,4.0079		368/2300	80865948	183,4383	692	1591	2283	SO:0001819	synonymous_variant	374462	exon5			ATTTACAATGTAT	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.1092A>G	12.37:g.80865948A>G		120.0	0.0	0		116.0	53.0	0.456897	NM_001145026		Silent	SNP	ENST00000266688.5	37		68	0.031135531135531136	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	44	0.05804749340369393	A	2.127	-0.400012	0.04865	0.010838	0.052797	ENSG00000139304	ENST00000532722	.	.	.	5.62	-3.25	0.05079	.	.	.	.	.	T	0.11153	0.0272	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31586	-0.9938	4	.	.	.	.	9.1629	0.37035	0.3104:0.5126:0.177:0.0	rs61729291	.	.	.	R	65	.	.	Q	+	2	0	PTPRQ	79390079	0.154000	0.22792	0.313000	0.25210	0.303000	0.27691	0.222000	0.17699	-0.723000	0.04915	-0.267000	0.10333	CAA	A|0.969;G|0.031	0.031	strong		0.398	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
SYNE1	23345	hgsc.bcm.edu	37	6	152532702	152532702	+	Missense_Mutation	SNP	T	T	C	rs35763277	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152532702T>C	ENST00000367255.5	-	124	23117	c.22516A>G	c.(22516-22518)Agt>Ggt	p.S7506G	SYNE1_ENST00000356820.4_Missense_Mutation_p.S2030G|SYNE1_ENST00000423061.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000448038.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000341594.5_Missense_Mutation_p.S7118G|SYNE1_ENST00000265368.4_Missense_Mutation_p.S7506G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7506			S -> G (in dbSNP:rs35763277).		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGCTGACGACTGAACATCTCG	0.328										HNSCC(10;0.0054)			T|||	23	0.00459265	0.0008	0.0072	5008	,	,		17739	0.0		0.0169	False		,,,				2504	0.0				p.S7506G		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A22516G						PASS	.	T	GLY/SER,GLY/SER	18,4388	26.2+/-53.5	0,18,2185	83.0	82.0	82.0		22303,22516	5.6	1.0	6	dbSNP_126	82	147,8453	71.3+/-133.9	2,143,4155	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	56,56	2,161,6340	CC,CT,TT		1.7093,0.4085,1.2686	probably-damaging,probably-damaging	7435/8750,7506/8798	152532702	165,12841	2203	4300	6503	SO:0001583	missense	23345	exon124			GACGACTGAACAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.22516A>G	6.37:g.152532702T>C	ENSP00000356224:p.Ser7506Gly	64.0	0.0	0		55.0	34.0	0.618182	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	17	0.007783882783882784	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	13	0.017150395778364115	T	25.9	4.689644	0.88735	0.004085	0.017093	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.50813	1.3;0.73;1.3;1.3;1.3;1.3;0.73;0.73	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	T	0.61726	0.2370	M	0.70595	2.14	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.997;0.999;0.997	T	0.64863	-0.6307	10	0.54805	T	0.06	.	16.1197	0.81342	0.0:0.0:0.0:1.0	rs35763277;rs36215571	7506;7506;7435;7435	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	G	7506;152;7435;7506;7435;7118;2030;428	ENSP00000356224:S7506G;ENSP00000356226:S152G;ENSP00000396024:S7435G;ENSP00000265368:S7506G;ENSP00000390975:S7435G;ENSP00000341887:S7118G;ENSP00000349276:S2030G;ENSP00000356220:S428G	ENSP00000265368:S7506G	S	-	1	0	SYNE1	152574395	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.941000	0.87700	2.257000	0.74773	0.455000	0.32223	AGT	T|0.988;C|0.012	0.012	strong		0.328	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
MMP24	10893	hgsc.bcm.edu	37	20	33855126	33855126	+	Silent	SNP	C	C	T	rs560750597		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:33855126C>T	ENST00000246186.6	+	6	1183	c.1098C>T	c.(1096-1098)ctC>ctT	p.L366L	MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|RP4-614O4.11_ENST00000444717.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000433764.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	366					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GGCCGCCCCTCGGGGACCGGC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		15710	0.0		0.0	False		,,,				2504	0.001				p.L366L		Atlas-SNP	.											.	MMP24	35	.	0			c.C1098T						PASS	.						20.0	25.0	23.0					20																	33855126		1916	4120	6036	SO:0001819	synonymous_variant	10893	exon6			GCCCCTCGGGGAC	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"""membrane-type 5 matrix metalloproteinase"""	604871	"""matrix metalloproteinase 24 (membrane-inserted)"""			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.1098C>T	20.37:g.33855126C>T		85.0	0.0	0		97.0	4.0	0.0412371	NM_006690	B7ZBG8|Q9H440	Silent	SNP	ENST00000246186.6	37	CCDS46593.1																																																																																			.	.	none		0.632	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690	
FLAD1	80308	hgsc.bcm.edu	37	1	154956487	154956487	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154956487C>A	ENST00000292180.3	+	1	639	c.317C>A	c.(316-318)tCt>tAt	p.S106Y	FLAD1_ENST00000368432.1_Missense_Mutation_p.S9Y|FLAD1_ENST00000368433.1_Missense_Mutation_p.S106Y|FLAD1_ENST00000487371.1_3'UTR|FLAD1_ENST00000315144.10_Missense_Mutation_p.S9Y|FLAD1_ENST00000368431.3_5'UTR	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	106					FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCTGAACTTTCTCCGGGGCGC	0.597																																					p.S106Y		Atlas-SNP	.											.	FLAD1	52	.	0			c.C317A						PASS	.						29.0	28.0	28.0					1																	154956487		2203	4300	6503	SO:0001583	missense	80308	exon1			AACTTTCTCCGGG		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"""Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)"", ""FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)"", ""flavin adenine dinucleotide synthetase"""				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.317C>A	1.37:g.154956487C>A	ENSP00000292180:p.Ser106Tyr	102.0	0.0	0		103.0	31.0	0.300971	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	37	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.248705	0.39797	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000292180	.	.	.	5.3	5.3	0.74995	Molybdopterin binding (1);	0.385773	0.26016	N	0.026854	T	0.38295	0.1035	N	0.20986	0.625	0.80722	D	1	B	0.22080	0.064	B	0.19391	0.025	T	0.33701	-0.9858	9	0.54805	T	0.06	-14.8505	17.1337	0.86733	0.0:1.0:0.0:0.0	.	106	Q8NFF5	FAD1_HUMAN	Y	106;9;9;106	.	ENSP00000292180:S106Y	S	+	2	0	FLAD1	153223111	0.035000	0.19736	0.576000	0.28549	0.262000	0.26303	1.899000	0.39818	2.655000	0.90218	0.555000	0.69702	TCT	.	.	none		0.597	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207	
C3orf17	25871	hgsc.bcm.edu	37	3	112724619	112724619	+	Missense_Mutation	SNP	A	A	G	rs7628368	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112724619A>G	ENST00000314400.5	-	9	1659	c.1468T>C	c.(1468-1470)Tca>Cca	p.S490P	C3orf17_ENST00000472762.1_5'Flank|C3orf17_ENST00000393857.2_Missense_Mutation_p.S354P|C3orf17_ENST00000383675.2_Missense_Mutation_p.S420P	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	490			S -> P (in dbSNP:rs7628368). {ECO:0000269|PubMed:17974005}.		negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						GTACAGTGTGAGAGTCTCCAC	0.433													A|||	232	0.0463259	0.1218	0.0231	5008	,	,		20084	0.003		0.0308	False		,,,				2504	0.0215				p.S490P		Atlas-SNP	.											C3orf17,lymph_node,lymphoid_neoplasm,0,1	C3orf17	37	1	0			c.T1468C						PASS	.	A	PRO/SER	487,3919	228.1+/-243.1	31,425,1747	120.0	110.0	114.0		1468	0.4	0.0	3	dbSNP_116	114	298,8302	108.8+/-169.4	5,288,4007	yes	missense	C3orf17	NM_015412.3	74	36,713,5754	GG,GA,AA		3.4651,11.0531,6.0357	possibly-damaging	490/568	112724619	785,12221	2203	4300	6503	SO:0001583	missense	25871	exon9			AGTGTGAGAGTCT	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.1468T>C	3.37:g.112724619A>G	ENSP00000320251:p.Ser490Pro	129.0	0.0	0		116.0	65.0	0.560345	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Missense_Mutation	SNP	ENST00000314400.5	37	CCDS33824.1	85	0.03891941391941392	47	0.09552845528455285	13	0.03591160220994475	0	0.0	25	0.032981530343007916	A	18.01	3.528189	0.64860	0.110531	0.034651	ENSG00000163608	ENST00000314400;ENST00000383675;ENST00000412848;ENST00000393857	T;T;T	0.40756	1.02;1.02;1.02	5.9	0.438	0.16560	.	0.700302	0.13762	N	0.364499	T	0.01558	0.0050	L	0.59436	1.845	0.09310	N	1	P;P;D;D	0.61080	0.911;0.948;0.989;0.989	P;P;P;P	0.58454	0.63;0.718;0.839;0.776	T	0.04178	-1.0971	10	0.66056	D	0.02	-3.5088	13.1573	0.59524	0.3745:0.6255:0.0:0.0	rs7628368;rs52792426;rs7628368	379;287;420;490	E7EN80;E7EQH6;Q6NW34-2;Q6NW34	.;.;.;CC017_HUMAN	P	490;420;137;354	ENSP00000320251:S490P;ENSP00000373173:S420P;ENSP00000377438:S354P	ENSP00000320251:S490P	S	-	1	0	C3orf17	114207309	0.003000	0.15002	0.001000	0.08648	0.131000	0.20780	0.157000	0.16402	0.120000	0.18254	-0.291000	0.09656	TCA	A|0.949;G|0.051	0.051	strong		0.433	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412	
TRIM45	80263	hgsc.bcm.edu	37	1	117659283	117659283	+	Missense_Mutation	SNP	C	C	T	rs61758105	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117659283C>T	ENST00000256649.4	-	3	1833	c.1307G>A	c.(1306-1308)gGa>gAa	p.G436E	TRIM45_ENST00000369464.3_Missense_Mutation_p.G418E|TRIM45_ENST00000369461.3_Missense_Mutation_p.G379E	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	436					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		AACGTTGTCTCCTCCCCTGCC	0.473													C|||	56	0.0111821	0.0	0.0663	5008	,	,		18984	0.0		0.006	False		,,,				2504	0.0041				p.G436E		Atlas-SNP	.											.	TRIM45	55	.	0			c.G1307A						PASS	.	C	GLU/GLY,GLU/GLY	18,4388	25.3+/-52.1	0,18,2185	92.0	86.0	88.0		1253,1307	5.1	1.0	1	dbSNP_129	88	137,8463	68.7+/-131.2	2,133,4165	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	98,98	2,151,6350	TT,TC,CC		1.593,0.4085,1.1918	probably-damaging,probably-damaging	418/563,436/581	117659283	155,12851	2203	4300	6503	SO:0001583	missense	80263	exon3			TTGTCTCCTCCCC		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1307G>A	1.37:g.117659283C>T	ENSP00000256649:p.Gly436Glu	80.0	0.0	0		73.0	40.0	0.547945	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	21	0.009615384615384616	0	0.0	16	0.04419889502762431	0	0.0	5	0.006596306068601583	C	25.2	4.612106	0.87258	0.004085	0.01593	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.85171	-1.95;-1.95;-1.95	5.09	5.09	0.68999	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92021	0.7472	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91709	0.5380	10	0.46703	T	0.11	-17.7023	15.8106	0.78561	0.0:1.0:0.0:0.0	rs61758105	418;436	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	E	436;418;379	ENSP00000256649:G436E;ENSP00000358476:G418E;ENSP00000358473:G379E	ENSP00000256649:G436E	G	-	2	0	TRIM45	117460806	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	6.277000	0.72608	2.646000	0.89796	0.563000	0.77884	GGA	C|0.989;T|0.011	0.011	strong		0.473	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
MTNR1A	4543	hgsc.bcm.edu	37	4	187455399	187455399	+	Missense_Mutation	SNP	C	C	T	rs28383653	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187455399C>T	ENST00000307161.5	-	2	698	c.497G>A	c.(496-498)gGg>gAg	p.G166E	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	166					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CTGGAGAGTCCCTGCACGGAG	0.607													C|||	17	0.00339457	0.0015	0.0086	5008	,	,		18017	0.0		0.0089	False		,,,				2504	0.0				p.G166E		Atlas-SNP	.											.	MTNR1A	46	.	0			c.G497A						PASS	.	C	GLU/GLY	13,4393	20.2+/-43.8	0,13,2190	127.0	103.0	111.0		497	4.1	0.1	4	dbSNP_125	111	139,8461	69.7+/-132.2	1,137,4162	yes	missense	MTNR1A	NM_005958.3	98	1,150,6352	TT,TC,CC		1.6163,0.2951,1.1687	possibly-damaging	166/351	187455399	152,12854	2203	4300	6503	SO:0001583	missense	4543	exon2			AGAGTCCCTGCAC		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.497G>A	4.37:g.187455399C>T	ENSP00000302811:p.Gly166Glu	71.0	0.0	0		69.0	33.0	0.478261	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	37	CCDS3848.1	22	0.010073260073260074	3	0.006097560975609756	7	0.019337016574585635	2	0.0034965034965034965	10	0.013192612137203167	C	14.72	2.619115	0.46736	0.002951	0.016163	ENSG00000168412	ENST00000307161	T	0.39592	1.07	4.96	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.43478	0.1249	M	0.82630	2.6	0.80722	D	1	D	0.55172	0.97	P	0.59012	0.85	T	0.56214	-0.8016	10	0.13108	T	0.6	-14.904	15.3219	0.74129	0.0:0.8602:0.1398:0.0	rs28383653	166	P48039	MTR1A_HUMAN	E	166	ENSP00000302811:G166E	ENSP00000302811:G166E	G	-	2	0	MTNR1A	187692393	0.993000	0.37304	0.053000	0.19242	0.019000	0.09904	3.190000	0.50973	2.295000	0.77249	0.655000	0.94253	GGG	C|0.988;T|0.012	0.012	strong		0.607	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
SLC26A7	115111	hgsc.bcm.edu	37	8	92330561	92330561	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:92330561T>C	ENST00000276609.3	+	5	834	c.595T>C	c.(595-597)Ttg>Ctg	p.L199L	SLC26A7_ENST00000523719.1_Silent_p.L199L|SLC26A7_ENST00000309536.2_Silent_p.L199L	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			CAAATATCTCTTGGGAATGAA	0.438																																					p.L199L		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T595C						PASS	.						128.0	128.0	128.0					8																	92330561		2203	4300	6503	SO:0001819	synonymous_variant	115111	exon5			TATCTCTTGGGAA	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"""Solute carriers"""	14467	protein-coding gene	gene with protein product		608479	"""solute carrier family 26, member 7"""			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.595T>C	8.37:g.92330561T>C		101.0	0.0	0		86.0	10.0	0.116279	NM_134266		Silent	SNP	ENST00000276609.3	37	CCDS6254.1																																																																																			.	.	none		0.438	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1		
DNAJC13	23317	hgsc.bcm.edu	37	3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	rs55825559	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:132221139C>T	ENST00000260818.6	+	40	4791	c.4543C>T	c.(4543-4545)Ccc>Tcc	p.P1515S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1515			P -> S (in dbSNP:rs55825559).		osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TCAGAGTATTCCCCGCGTAGC	0.413													C|||	60	0.0119808	0.0	0.0245	5008	,	,		15388	0.0		0.0368	False		,,,				2504	0.0061				p.P1515S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4543T						PASS	.	C	SER/PRO	26,4380	32.6+/-62.9	0,26,2177	117.0	113.0	115.0		4543	5.8	1.0	3	dbSNP_129	115	239,8361	94.5+/-156.4	5,229,4066	yes	missense	DNAJC13	NM_015268.3	74	5,255,6243	TT,TC,CC		2.7791,0.5901,2.0375	benign	1515/2244	132221139	265,12741	2203	4300	6503	SO:0001583	missense	23317	exon40			AGTATTCCCCGCG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4543C>T	3.37:g.132221139C>T	ENSP00000260818:p.Pro1515Ser	125.0	0.0	0		115.0	59.0	0.513043	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	C	14.92	2.678748	0.47886	0.005901	0.027791	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52057	0.68	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.69185	2.1	0.54753	D	0.999985	B	0.20368	0.044	B	0.15870	0.014	T	0.17653	-1.0362	10	0.40728	T	0.16	.	16.3288	0.82997	0.0:0.868:0.132:0.0	rs55825559;rs61748104	1515	O75165	DJC13_HUMAN	S	1515;162	ENSP00000260818:P1515S	ENSP00000260818:P1515S	P	+	1	0	DNAJC13	133703829	1.000000	0.71417	0.998000	0.56505	0.614000	0.37383	4.644000	0.61397	2.734000	0.93682	0.650000	0.86243	CCC	C|0.981;T|0.019	0.019	strong		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
ASXL3	80816	hgsc.bcm.edu	37	18	31326554	31326554	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:31326554C>T	ENST00000269197.5	+	12	6742	c.6742C>T	c.(6742-6744)Cga>Tga	p.R2248*		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CCTGGTTGTACGATAAGAGCT	0.458																																					p.R2248X		Atlas-SNP	.											ASXL3_ENST00000269197,NS,carcinoma,-1,1	ASXL3	405	1	0			c.C6742T						PASS	.						109.0	104.0	106.0					18																	31326554		1994	4172	6166	SO:0001587	stop_gained	80816	exon12			GTTGTACGATAAG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6742C>T	18.37:g.31326554C>T	ENSP00000269197:p.Arg2248*	21.0	0.0	0		20.0	7.0	0.35	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Nonsense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	46	12.156967	0.99642	.	.	ENSG00000141431	ENST00000269197	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.49051	D	0.999744	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	.	.	.	X	2248	.	ENSP00000269197:R2248X	R	+	1	2	ASXL3	29580552	0.999000	0.42202	0.998000	0.56505	0.883000	0.51084	3.717000	0.54911	2.854000	0.98071	0.655000	0.94253	CGA	.	.	none		0.458	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
SLC12A3	6559	hgsc.bcm.edu	37	16	56904075	56904075	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:56904075C>T	ENST00000563236.1	+	5	694	c.669C>T	c.(667-669)ttC>ttT	p.F223F	SLC12A3_ENST00000566786.1_Silent_p.F222F|SLC12A3_ENST00000262502.5_Silent_p.F222F|SLC12A3_ENST00000438926.2_Silent_p.F223F			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	223					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GCCTCATTTTCGCTTTCGCCA	0.642																																					p.F223F		Atlas-SNP	.											.	SLC12A3	99	.	0			c.C669T						PASS	.						69.0	68.0	68.0					16																	56904075		2198	4300	6498	SO:0001819	synonymous_variant	6559	exon5			CATTTTCGCTTTC		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.669C>T	16.37:g.56904075C>T		90.0	0.0	0		80.0	4.0	0.05	NM_001126108	A8MSJ2|C9JNN9	Silent	SNP	ENST00000563236.1	37	CCDS58464.1																																																																																			.	.	none		0.642	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
INPP5B	3633	hgsc.bcm.edu	37	1	38343863	38343863	+	Silent	SNP	G	G	A	rs141357169	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:38343863G>A	ENST00000373026.1	-	15	1914	c.1914C>T	c.(1912-1914)atC>atT	p.I638I	INPP5B_ENST00000373024.3_Silent_p.I558I|INPP5B_ENST00000373023.2_Silent_p.I638I|INPP5B_ENST00000458109.2_3'UTR|INPP5B_ENST00000373027.1_Silent_p.I394I			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	638	5-phosphatase. {ECO:0000250}.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CACCTACCCCGATGTCAAACA	0.483													G|||	3	0.000599042	0.0	0.0	5008	,	,		20679	0.0		0.003	False		,,,				2504	0.0				p.I558I		Atlas-SNP	.											.	INPP5B	76	.	0			c.C1674T						PASS	.	G		0,4002		0,0,2001	98.0	100.0	99.0		1674	-2.4	1.0	1	dbSNP_134	99	21,8325		0,21,4152	no	coding-synonymous	INPP5B	NM_005540.2		0,21,6153	AA,AG,GG		0.2516,0.0,0.1701		558/914	38343863	21,12327	2001	4173	6174	SO:0001819	synonymous_variant	3633	exon16			TACCCCGATGTCA	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.1914C>T	1.37:g.38343863G>A		118.0	0.0	0		92.0	37.0	0.402174	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37																																																																																				G|0.997;A|0.003	0.003	strong		0.483	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
BRD4	23476	hgsc.bcm.edu	37	19	15349962	15349962	+	Silent	SNP	G	G	A	rs118000160	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15349962G>A	ENST00000263377.2	-	18	3911	c.3690C>T	c.(3688-3690)gcC>gcT	p.A1230A		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1230	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TCTCCCGAGCGGCGCGGCGGA	0.657			T	C15orf55	lethal midline carcinoma of young people								g|||	13	0.00259585	0.0008	0.0029	5008	,	,		15419	0.0		0.004	False		,,,				2504	0.0061				p.A1230A		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C3690T						PASS	.			4,4402	8.1+/-20.4	0,4,2199	29.0	31.0	30.0		3690	-9.5	0.0	19	dbSNP_132	30	66,8532	38.8+/-94.9	0,66,4233	no	coding-synonymous	BRD4	NM_058243.2		0,70,6432	AA,AG,GG		0.7676,0.0908,0.5383		1230/1363	15349962	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	23476	exon18			CCGAGCGGCGCGG	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3690C>T	19.37:g.15349962G>A		116.0	0.0	0		104.0	55.0	0.528846	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																			G|0.997;A|0.003	0.003	strong		0.657	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
CIITA	4261	hgsc.bcm.edu	37	16	11000862	11000862	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11000862G>T	ENST00000324288.8	+	11	1646	c.1513G>T	c.(1513-1515)Gaa>Taa	p.E505*	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	505	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CGAGGAGCTGGAAGCGCAAGA	0.647			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.E505X		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G1513T						PASS	.						61.0	65.0	63.0					16																	11000862		2197	4300	6497	SO:0001587	stop_gained	4261	exon11			GAGCTGGAAGCGC	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1513G>T	16.37:g.11000862G>T	ENSP00000316328:p.Glu505*	33.0	0.0	0		41.0	19.0	0.463415	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Nonsense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	33	5.202661	0.94997	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	.	.	.	5.27	5.27	0.74061	.	0.000000	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	12.6857	0.56946	0.0:0.2738:0.7262:0.0	.	.	.	.	X	505;457	.	ENSP00000316328:E505X	E	+	1	0	CIITA	10908363	1.000000	0.71417	0.223000	0.23860	0.234000	0.25298	5.332000	0.65911	2.442000	0.82660	0.561000	0.74099	GAA	.	.	none		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
DCST2	127579	hgsc.bcm.edu	37	1	155004092	155004092	+	Missense_Mutation	SNP	C	C	T	rs373275652		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155004092C>T	ENST00000368424.3	-	4	755	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000295542.1_5'Flank|DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000423025.2_5'Flank|DCST2_ENST00000295536.5_Missense_Mutation_p.V233M	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	233						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGCATGAGCACGTAACACAGG	0.592																																					p.V233M		Atlas-SNP	.											.	DCST2	80	.	0			c.G697A						PASS	.	C	MET/VAL	0,4406		0,0,2203	147.0	115.0	126.0		697	2.2	0.9	1		126	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCST2	NM_144622.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	233/774	155004092	1,13005	2203	4300	6503	SO:0001583	missense	127579	exon4			TGAGCACGTAACA	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.697G>A	1.37:g.155004092C>T	ENSP00000357409:p.Val233Met	161.0	0.0	0		165.0	78.0	0.472727	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620203	0.46736	0.0	1.16E-4	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.26373	1.74;1.78	5.57	2.18	0.27775	.	0.652606	0.13132	N	0.411331	T	0.06234	0.0161	L	0.29908	0.895	0.09310	N	0.999991	D	0.54601	0.967	B	0.39660	0.306	T	0.18681	-1.0329	10	0.30078	T	0.28	-10.1195	7.9825	0.30192	0.0:0.6559:0.0:0.3441	.	233	Q5T1A1	DCST2_HUMAN	M	233	ENSP00000357409:V233M;ENSP00000295536:V233M	ENSP00000295536:V233M	V	-	1	0	DCST2	153270716	0.149000	0.22717	0.913000	0.36048	0.967000	0.64934	0.384000	0.20668	0.702000	0.31825	0.655000	0.94253	GTG	.	.	none		0.592	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
ZNF451	26036	hgsc.bcm.edu	37	6	56966040	56966040	+	Intron	SNP	T	T	C	rs188982073	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56966040T>C	ENST00000370706.4	+	3	430				ZNF451_ENST00000491832.2_Intron|ZNF451_ENST00000370702.1_Intron|ZNF451_ENST00000357489.3_Intron|ZNF451_ENST00000370708.4_Silent_p.L276L	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AAGGGTGACATTACAATCTGA	0.438													T|||	2	0.000399361	0.0	0.0014	5008	,	,		22089	0.0		0.001	False		,,,				2504	0.0				p.L276L		Atlas-SNP	.											.	ZNF451	181	.	0			c.T826C						PASS	.																																			SO:0001627	intron_variant	26036	exon4			GTGACATTACAAT	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.186+2101T>C	6.37:g.56966040T>C		56.0	0.0	0		53.0	28.0	0.528302	NM_001257273	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Silent	SNP	ENST00000370706.4	37	CCDS43477.1																																																																																			T|0.999;C|0.001	0.001	strong		0.438	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	
MAFG	4097	hgsc.bcm.edu	37	17	79880565	79880565	+	Silent	SNP	G	G	A	rs61752690	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79880565G>A	ENST00000357736.4	-	3	620	c.405C>T	c.(403-405)gcC>gcT	p.A135A	MAFG_ENST00000392366.3_Silent_p.A135A|RP11-498C9.12_ENST00000580897.1_RNA	NM_002359.3|NM_032711.3	NP_002350.1|NP_116100.2	O15525	MAFG_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G	135					adult behavior (GO:0030534)|blood coagulation (GO:0007596)|in utero embryonic development (GO:0001701)|regulation of cell proliferation (GO:0042127)|regulation of cellular pH (GO:0030641)|regulation of epidermal cell differentiation (GO:0045604)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|lung(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GCCCCAGGCCGGCGGCAAGGG	0.716													G|||	6	0.00119808	0.0	0.0014	5008	,	,		11901	0.0		0.003	False		,,,				2504	0.002				p.A135A		Atlas-SNP	.											.	MAFG	9	.	0			c.C405T						PASS	.	G	,	5,4303		0,5,2149	10.0	11.0	10.0		405,405	-2.1	0.0	17	dbSNP_129	10	60,8350		0,60,4145	no	coding-synonymous,coding-synonymous	MAFG	NM_002359.3,NM_032711.3	,	0,65,6294	AA,AG,GG		0.7134,0.1161,0.5111	,	135/163,135/163	79880565	65,12653	2154	4205	6359	SO:0001819	synonymous_variant	4097	exon3			CAGGCCGGCGGCA	AF059195	CCDS11793.1	17q25.3	2013-07-09	2013-07-09		ENSG00000197063	ENSG00000197063			6781	protein-coding gene	gene with protein product	"""transcription factor MafG"", ""basic leucine zipper transcription factor MafG"""	602020				9763667	Standard	NM_002359		Approved	MGC13090, MGC20149	uc002kcm.3	O15525		ENST00000357736.4:c.405C>T	17.37:g.79880565G>A		14.0	0.0	0		12.0	7.0	0.583333	NM_032711		Silent	SNP	ENST00000357736.4	37	CCDS11793.1																																																																																			A|0.002;G|0.998	0.002	strong		0.716	MAFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439980.1	NM_002359	
R3HDM1	23518	hgsc.bcm.edu	37	2	136467080	136467080	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:136467080A>T	ENST00000264160.4	+	21	2802	c.2432A>T	c.(2431-2433)cAg>cTg	p.Q811L	R3HDM1_ENST00000409478.1_Missense_Mutation_p.Q683L|R3HDM1_ENST00000409606.1_Missense_Mutation_p.Q812L|R3HDM1_ENST00000410054.1_Missense_Mutation_p.Q756L|R3HDM1_ENST00000329971.3_Missense_Mutation_p.Q682L	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	811							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		TGCAGTTCCCAGCAGCTTCAA	0.388																																					p.Q811L		Atlas-SNP	.											.	R3HDM1	84	.	0			c.A2432T						PASS	.						126.0	110.0	115.0					2																	136467080		2203	4300	6503	SO:0001583	missense	23518	exon21			GTTCCCAGCAGCT	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.2432A>T	2.37:g.136467080A>T	ENSP00000264160:p.Gln811Leu	253.0	0.0	0		206.0	87.0	0.42233	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.31|12.31	1.899556|1.899556	0.33535|0.33535	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606|ENST00000445855	T;T;T;T;T|.	0.33654|.	1.41;1.4;1.41;1.4;1.4|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.136231|.	0.51477|.	N|.	0.000087|.	T|T	0.71533|0.71533	0.3351|0.3351	M|M	0.61703|0.61703	1.905|1.905	0.48288|0.48288	D|D	0.999627|0.999627	D;B;B;B|.	0.53745|.	0.962;0.156;0.057;0.057|.	D;B;B;B|.	0.66716|.	0.946;0.034;0.023;0.023|.	T|T	0.70637|0.70637	-0.4817|-0.4817	10|5	0.34782|.	T|.	0.22|.	-0.8796|-0.8796	15.5092|15.5092	0.75766|0.75766	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	683;812;756;811|.	G5E9G8;E9PBB4;E9PG42;Q15032|.	.;.;.;R3HD1_HUMAN|.	L|C	683;811;682;756;812|107	ENSP00000386457:Q683L;ENSP00000264160:Q811L;ENSP00000331396:Q682L;ENSP00000386877:Q756L;ENSP00000387010:Q812L|.	ENSP00000264160:Q811L|.	Q|S	+|+	2|1	0|0	R3HDM1|R3HDM1	136183550|136183550	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.042000|7.042000	0.76565|0.76565	2.138000|2.138000	0.66242|0.66242	0.524000|0.524000	0.50904|0.50904	CAG|AGC	.	.	none		0.388	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	
FGL1	2267	hgsc.bcm.edu	37	8	17731876	17731876	+	Silent	SNP	A	A	G	rs34871936	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17731876A>G	ENST00000398056.2	-	6	1214	c.399T>C	c.(397-399)ttT>ttC	p.F133F	FGL1_ENST00000381841.2_Silent_p.F133F|FGL1_ENST00000427924.1_Silent_p.F133F|FGL1_ENST00000398054.1_Silent_p.F133F|FGL1_ENST00000522444.1_Silent_p.F133F|FGL1_ENST00000518650.1_Silent_p.F133F|FGL1_ENST00000381840.2_Silent_p.F133F			Q08830	FGL1_HUMAN	fibrinogen-like 1	133	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		CACACCTGTTAAAGTTTTCAC	0.368													A|||	25	0.00499201	0.0015	0.0072	5008	,	,		17596	0.0		0.0119	False		,,,				2504	0.0061				p.F133F		Atlas-SNP	.											.	FGL1	31	.	0			c.T399C						PASS	.	A	,,,	13,4393	20.2+/-43.8	0,13,2190	116.0	108.0	111.0		399,399,399,399	1.4	1.0	8	dbSNP_126	111	117,8483	63.1+/-125.2	2,113,4185	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGL1	NM_004467.3,NM_147203.2,NM_201552.1,NM_201553.1	,,,	2,126,6375	GG,GA,AA		1.3605,0.2951,0.9995	,,,	133/313,133/313,133/313,133/313	17731876	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2267	exon5			CCTGTTAAAGTTT	D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"""Fibrinogen C domain containing"""	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.399T>C	8.37:g.17731876A>G		115.0	0.0	0		102.0	45.0	0.441176	NM_201553	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Silent	SNP	ENST00000398056.2	37	CCDS6004.1																																																																																			A|0.990;G|0.010	0.010	strong		0.368	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467	
GNGT1	2792	hgsc.bcm.edu	37	7	93540153	93540153	+	Missense_Mutation	SNP	G	G	A	rs17243826	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:93540153G>A	ENST00000248572.5	+	3	296	c.148G>A	c.(148-150)Gag>Aag	p.E50K	GNGT1_ENST00000455502.1_3'UTR|GNGT1_ENST00000429473.1_Missense_Mutation_p.E50K	NM_021955.3	NP_068774.1	P63211	GBG1_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	50			E -> K (in dbSNP:rs17243826).		cardiac muscle cell apoptotic process (GO:0010659)|cellular response to hypoxia (GO:0071456)|eye photoreceptor cell development (GO:0042462)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			ACGATCTGGCGAGGATCCACT	0.388													G|||	143	0.0285543	0.0166	0.0519	5008	,	,		15953	0.0		0.0487	False		,,,				2504	0.0368				p.E50K		Atlas-SNP	.											.	GNGT1	12	.	0			c.G148A						PASS	.	G	LYS/GLU	112,4294	80.9+/-119.3	8,96,2099	86.0	84.0	85.0		148	5.6	0.6	7	dbSNP_123	85	442,8158	133.0+/-190.5	27,388,3885	yes	missense	GNGT1	NM_021955.3	56	35,484,5984	AA,AG,GG		5.1395,2.542,4.2596	possibly-damaging	50/75	93540153	554,12452	2203	4300	6503	SO:0001583	missense	2792	exon3			TCTGGCGAGGATC		CCDS5633.1	7q21.3	2008-07-18			ENSG00000127928	ENSG00000127928			4411	protein-coding gene	gene with protein product		189970				8661128	Standard	NM_021955		Approved	GNG1	uc003unc.1	P63211	OTTHUMG00000022908	ENST00000248572.5:c.148G>A	7.37:g.93540153G>A	ENSP00000248572:p.Glu50Lys	97.0	0.0	0		101.0	39.0	0.386139	NM_021955	A4D1H2|O43835|Q08447|Q16026|Q6LCP6	Missense_Mutation	SNP	ENST00000248572.5	37	CCDS5633.1	63	0.028846153846153848	12	0.024390243902439025	21	0.058011049723756904	0	0.0	30	0.0395778364116095	G	16.90	3.248745	0.59103	0.02542	0.051395	ENSG00000127928	ENST00000248572;ENST00000429473	T;T	0.19394	2.15;2.15	5.6	5.6	0.85130	G-protein gamma domain (5);	0.052380	0.64402	D	0.000001	T	0.01730	0.0055	.	.	.	0.80722	D	1	P	0.43094	0.799	B	0.36244	0.22	T	0.05225	-1.0898	9	0.24483	T	0.36	-18.2019	18.7588	0.91842	0.0:0.0:1.0:0.0	rs17243826;rs17243826	50	P63211	GBG1_HUMAN	K	50	ENSP00000248572:E50K;ENSP00000388777:E50K	ENSP00000248572:E50K	E	+	1	0	GNGT1	93378089	1.000000	0.71417	0.597000	0.28824	0.172000	0.22775	6.792000	0.75125	2.809000	0.96659	0.655000	0.94253	GAG	A|0.023;C|0.029;G|0.948	0.023	strong		0.388	GNGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254718.2	NM_021955	
IRF1	3659	hgsc.bcm.edu	37	5	131825083	131825083	+	Splice_Site	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131825083C>A	ENST00000245414.4	-	2	346		c.e2+1		IRF1_ENST00000463784.1_Intron|IRF1_ENST00000405885.2_Splice_Site	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1						apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		GTTACACTCACTTTATTAATC	0.473																																					.		Atlas-SNP	.											.	IRF1	26	.	0			c.87+1G>T						PASS	.						83.0	85.0	85.0					5																	131825083		2202	4300	6502	SO:0001630	splice_region_variant	3659	exon3			CACTCACTTTATT		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"""interferon regulatory factor-1"""	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.87+1G>T	5.37:g.131825083C>A		66.0	0.0	0		49.0	21.0	0.428571	NM_002198	Q96GG7	Splice_Site	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794920	0.90453	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.96	0.97242	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IRF1	131852982	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.373000	0.79623	2.793000	0.96121	0.561000	0.74099	.	.	.	none		0.473	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	Intron
SGIP1	84251	hgsc.bcm.edu	37	1	67148009	67148009	+	Silent	SNP	G	G	A	rs61798708	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67148009G>A	ENST00000371037.4	+	15	1349	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000237247.6_Silent_p.S428S|SGIP1_ENST00000371039.1_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	424	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						CTGTGGTTTCGTCCCCCGGAC	0.552													G|||	16	0.00319489	0.0015	0.0014	5008	,	,		18121	0.005		0.007	False		,,,				2504	0.001				p.S424S		Atlas-SNP	.											.	SGIP1	272	.	0			c.G1272A						PASS	.	G		7,4399		0,7,2196	106.0	120.0	115.0		1272	-0.2	1.0	1	dbSNP_129	115	73,8527		0,73,4227	no	coding-synonymous	SGIP1	NM_032291.2		0,80,6423	AA,AG,GG		0.8488,0.1589,0.6151		424/829	67148009	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	84251	exon15			GGTTTCGTCCCCC	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.1272G>A	1.37:g.67148009G>A		109.0	0.0	0		106.0	45.0	0.424528	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Silent	SNP	ENST00000371037.4	37	CCDS30744.1																																																																																			G|0.994;A|0.006	0.006	strong		0.552	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291	
ALG3	10195	hgsc.bcm.edu	37	3	183958706	183958706	+	IGR	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183958706G>A	ENST00000397676.3	-	0	1528				EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000426955.2_Silent_p.V956V|VWA5B2_ENST00000273794.5_Silent_p.V738V|MIR1224_ENST00000408193.1_RNA|ALG3_ENST00000463495.1_5'Flank	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCCTGCAGGTGTGCAGCTCAG	0.607																																					p.V956V		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G2868A						PASS	.						41.0	40.0	40.0					3																	183958706		692	1591	2283	SO:0001628	intergenic_variant	90113	exon16			GCAGGTGTGCAGC	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823		3.37:g.183958706G>A		79.0	0.0	0		60.0	15.0	0.25	NM_138345	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	CCDS46968.1																																																																																			.	.	none		0.607	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
USH1C	10083	hgsc.bcm.edu	37	11	17552707	17552707	+	Silent	SNP	C	C	A	rs41282942	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17552707C>A	ENST00000318024.4	-	4	489	c.381G>T	c.(379-381)ggG>ggT	p.G127G	USH1C_ENST00000527720.1_Silent_p.G96G|USH1C_ENST00000005226.7_Silent_p.G127G|USH1C_ENST00000527020.1_Silent_p.G127G	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	127	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						TCACCTGGAGCCCGACGCTGT	0.642													C|||	7	0.00139776	0.0008	0.0014	5008	,	,		16949	0.001		0.003	False		,,,				2504	0.001				p.G127G		Atlas-SNP	.											.	USH1C	157	.	0			c.G381T						PASS	.	C	,	2,4398	4.2+/-10.8	0,2,2198	33.0	37.0	36.0		381,381	3.5	1.0	11	dbSNP_127	36	39,8547	25.1+/-72.6	0,39,4254	no	coding-synonymous,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	0,41,6452	AA,AC,CC		0.4542,0.0455,0.3157	,	127/553,127/900	17552707	41,12945	2200	4293	6493	SO:0001819	synonymous_variant	10083	exon4			CTGGAGCCCGACG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.381G>T	11.37:g.17552707C>A		65.0	0.0	0		75.0	36.0	0.48	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			C|0.998;A|0.002	0.002	strong		0.642	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
AMBRA1	55626	hgsc.bcm.edu	37	11	46456444	46456444	+	Silent	SNP	G	G	A	rs61999319	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:46456444G>A	ENST00000458649.2	-	13	3194	c.2776C>T	c.(2776-2778)Ctg>Ttg	p.L926L	AMBRA1_ENST00000426438.1_Silent_p.L897L|AMBRA1_ENST00000314845.3_Silent_p.L836L|AMBRA1_ENST00000534300.1_Silent_p.L866L|AMBRA1_ENST00000528950.1_Silent_p.L897L|AMBRA1_ENST00000298834.3_Silent_p.L866L|AMBRA1_ENST00000533727.1_Silent_p.L807L			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	926					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		TGGGGGGCCAGGGAGTACACT	0.572													G|||	38	0.00758786	0.003	0.0159	5008	,	,		20047	0.0		0.0229	False		,,,				2504	0.0				p.L929L		Atlas-SNP	.											.	AMBRA1	201	.	0			c.C2785T						PASS	.	G		21,4381	28.1+/-56.4	1,19,2181	79.0	68.0	71.0		2506	3.5	1.0	11	dbSNP_129	71	209,8389	89.4+/-151.6	1,207,4091	no	coding-synonymous	AMBRA1	NM_017749.2		2,226,6272	AA,AG,GG		2.4308,0.4771,1.7692		836/1209	46456444	230,12770	2201	4299	6500	SO:0001819	synonymous_variant	55626	exon15			GGGCCAGGGAGTA	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.2776C>T	11.37:g.46456444G>A		161.0	0.0	0		176.0	101.0	0.573864	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																				G|0.985;A|0.015	0.015	strong		0.572	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
EVPL	2125	hgsc.bcm.edu	37	17	74003525	74003525	+	Missense_Mutation	SNP	C	C	T	rs141706835		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74003525C>T	ENST00000301607.3	-	22	6014	c.5761G>A	c.(5761-5763)Gtc>Atc	p.V1921I	EVPL_ENST00000586740.1_Missense_Mutation_p.V1943I|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1921	Globular 2.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCCTTCTGGACGGCCTCGCCC	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		16834	0.0		0.0	False		,,,				2504	0.001				p.V1921I		Atlas-SNP	.											EVPL,colon,carcinoma,0,1	EVPL	155	1	0			c.G5761A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	47.0	41.0	43.0		5761	-7.3	0.1	17	dbSNP_134	43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	EVPL	NM_001988.2	29	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	1921/2034	74003525	3,13003	2203	4300	6503	SO:0001583	missense	2125	exon22			TCTGGACGGCCTC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.5761G>A	17.37:g.74003525C>T	ENSP00000301607:p.Val1921Ile	68.0	0.0	0		66.0	33.0	0.5	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	8.608	0.888553	0.17540	2.27E-4	2.33E-4	ENSG00000167880	ENST00000301607	T	0.66460	-0.21	5.48	-7.34	0.01427	.	0.382752	0.26463	N	0.024227	T	0.45013	0.1321	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.30605	0.039;0.287	B;B	0.23574	0.025;0.047	T	0.03121	-1.1070	10	0.24483	T	0.36	-16.312	19.1581	0.93520	0.0:0.8769:0.0:0.1231	.	1943;1921	B7ZLH8;Q92817	.;EVPL_HUMAN	I	1921	ENSP00000301607:V1921I	ENSP00000301607:V1921I	V	-	1	0	EVPL	71515120	0.000000	0.05858	0.123000	0.21794	0.698000	0.40448	-0.195000	0.09546	-1.270000	0.02433	-0.291000	0.09656	GTC	C|1.000;T|0.000	0.000	weak		0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
COL2A1	1280	hgsc.bcm.edu	37	12	48381394	48381394	+	Splice_Site	SNP	G	G	A	rs150865922	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48381394G>A	ENST00000380518.3	-	19	1385	c.1221C>T	c.(1219-1221)tcC>tcT	p.S407S	COL2A1_ENST00000337299.6_Splice_Site_p.S338S|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	407	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTGCACTTACGGAGGCACCAG	0.617													G|||	12	0.00239617	0.0	0.0029	5008	,	,		18272	0.0		0.0089	False		,,,				2504	0.001				p.S407S		Atlas-SNP	.											.	COL2A1	368	.	0			c.C1221T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	53.0	47.0	49.0		1221,1014	0.4	1.0	12	dbSNP_134	49	50,8548	29.6+/-80.5	0,50,4249	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	COL2A1	NM_001844.4,NM_033150.2	,	0,52,6450	AA,AG,GG		0.5815,0.0454,0.3999	,	407/1488,338/1419	48381394	52,12952	2203	4299	6502	SO:0001630	splice_region_variant	1280	exon19			ACTTACGGAGGCA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1221+1C>T	12.37:g.48381394G>A		30.0	0.0	0		28.0	12.0	0.428571	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																			G|0.997;A|0.003	0.003	strong		0.617	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	Silent
BCAN	63827	hgsc.bcm.edu	37	1	156616814	156616814	+	Missense_Mutation	SNP	C	C	G	rs115373136	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156616814C>G	ENST00000329117.5	+	3	649	c.313C>G	c.(313-315)Cgg>Ggg	p.R105G	BCAN_ENST00000361588.5_Missense_Mutation_p.R105G|RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	105	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGAGGCCTACCGGTTCCGCGT	0.682													C|||	28	0.00559105	0.0	0.0043	5008	,	,		14357	0.0		0.0199	False		,,,				2504	0.0051				p.R105G		Atlas-SNP	.											.	BCAN	174	.	0			c.C313G						PASS	.	C	GLY/ARG,GLY/ARG	8,4398	14.3+/-33.2	0,8,2195	47.0	35.0	39.0		313,313	2.5	1.0	1	dbSNP_132	39	116,8480	57.5+/-118.9	0,116,4182	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	125,125	0,124,6377	GG,GC,CC		1.3495,0.1816,0.9537	possibly-damaging,possibly-damaging	105/912,105/672	156616814	124,12878	2203	4298	6501	SO:0001583	missense	63827	exon3			GCCTACCGGTTCC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.313C>G	1.37:g.156616814C>G	ENSP00000331210:p.Arg105Gly	62.0	0.0	0		47.0	22.0	0.468085	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	C	14.87	2.664022	0.47572	0.001816	0.013495	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000361588	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	4.61	2.47	0.30058	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000061	T	0.64238	0.2580	L	0.53671	1.685	0.36444	D	0.865697	D;P	0.65815	0.995;0.856	D;B	0.67382	0.951;0.285	T	0.70353	-0.4895	10	0.87932	D	0	-20.2388	12.8011	0.57586	0.3062:0.6938:0.0:0.0	.	105;105	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	G	105	ENSP00000392731:R105G;ENSP00000331210:R105G;ENSP00000389898:R105G;ENSP00000354925:R105G	ENSP00000255029:R105G	R	+	1	2	BCAN	154883438	0.000000	0.05858	1.000000	0.80357	0.530000	0.34684	-0.350000	0.07721	1.088000	0.41272	0.455000	0.32223	CGG	C|0.989;G|0.011	0.011	strong		0.682	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
CARD11	84433	hgsc.bcm.edu	37	7	2984153	2984153	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2984153C>T	ENST00000396946.4	-	5	780	c.377G>A	c.(376-378)gGc>gAc	p.G126D	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	126					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.G119D(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GTGCGTGAGGCCCTCGTGGCC	0.617			Mis		DLBCL																																p.G126D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,colon,carcinoma,+1,4	CARD11	339	4	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G377A						PASS	.						57.0	54.0	55.0					7																	2984153		2203	4300	6503	SO:0001583	missense	84433	exon5			GTGAGGCCCTCGT	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.377G>A	7.37:g.2984153C>T	ENSP00000380150:p.Gly126Asp	45.0	0.0	0		63.0	25.0	0.396825	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601697	0.87055	.	.	ENSG00000198286	ENST00000396946	T	0.38077	1.16	4.24	4.24	0.50183	.	0.053038	0.85682	D	0.000000	T	0.58991	0.2161	M	0.72353	2.195	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.64041	-0.6500	10	0.54805	T	0.06	-41.4985	17.0013	0.86382	0.0:1.0:0.0:0.0	.	126	Q9BXL7	CAR11_HUMAN	D	126	ENSP00000380150:G126D	ENSP00000380150:G126D	G	-	2	0	CARD11	2950679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.273000	0.78527	2.071000	0.62044	0.655000	0.94253	GGC	.	.	none		0.617	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
SYNE1	23345	hgsc.bcm.edu	37	6	152668211	152668211	+	Missense_Mutation	SNP	A	A	G	rs111449472	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152668211A>G	ENST00000367255.5	-	73	12662	c.12061T>C	c.(12061-12063)Tgc>Cgc	p.C4021R	SYNE1_ENST00000423061.1_Missense_Mutation_p.C3950R|SYNE1_ENST00000448038.1_Missense_Mutation_p.C3950R|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.C4021R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4021					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCTGTGCTGCAGATCGCTGAG	0.483										HNSCC(10;0.0054)			A|||	27	0.00539137	0.003	0.0086	5008	,	,		18057	0.0		0.0119	False		,,,				2504	0.0051				p.C4021R		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T12061C						PASS	.	A	ARG/CYS,ARG/CYS	16,4390	22.3+/-47.3	0,16,2187	159.0	131.0	141.0		11848,12061	5.7	1.0	6	dbSNP_132	141	130,8470	66.0+/-128.3	1,128,4171	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	180,180	1,144,6358	GG,GA,AA		1.5116,0.3631,1.1226	probably-damaging,probably-damaging	3950/8750,4021/8798	152668211	146,12860	2203	4300	6503	SO:0001583	missense	23345	exon73			TGCTGCAGATCGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12061T>C	6.37:g.152668211A>G	ENSP00000356224:p.Cys4021Arg	116.0	0.0	0		104.0	42.0	0.403846	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	19	0.0086996336996337	3	0.006097560975609756	3	0.008287292817679558	0	0.0	13	0.017150395778364115	A	13.58	2.279409	0.40294	0.003631	0.015116	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000005	T	0.46425	0.1392	M	0.66939	2.045	0.80722	D	1	D;D;D;B	0.89917	1.0;1.0;1.0;0.0	D;D;D;B	0.91635	0.999;0.999;0.999;0.0	T	0.46816	-0.9164	10	0.54805	T	0.06	.	15.9869	0.80160	1.0:0.0:0.0:0.0	.	4021;4021;4021;3950	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	R	4021;3950;4021;3950	ENSP00000356224:C4021R;ENSP00000396024:C3950R;ENSP00000265368:C4021R;ENSP00000390975:C3950R	ENSP00000265368:C4021R	C	-	1	0	SYNE1	152709904	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.905000	0.92613	2.171000	0.68590	0.533000	0.62120	TGC	A|0.990;G|0.010	0.010	strong		0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
FHAD1	114827	hgsc.bcm.edu	37	1	15679393	15679393	+	Silent	SNP	G	G	A	rs35368057	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15679393G>A	ENST00000375998.4	+	18	2409	c.2409G>A	c.(2407-2409)gcG>gcA	p.A803A	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Silent_p.A767A|FHAD1_ENST00000314740.8_Silent_p.A56A|FHAD1_ENST00000375999.3_Silent_p.A803A|FHAD1_ENST00000358897.4_Silent_p.A803A			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	803										skin(1)|stomach(1)	2						GCAACATTGCGTACGAGAAAC	0.493													g|||	39	0.00778754	0.0151	0.0086	5008	,	,		23921	0.001		0.0119	False		,,,				2504	0.0				p.A803A		Atlas-SNP	.											.	FHAD1	78	.	0			c.G2409A						PASS	.	A		29,1355		0,29,663	116.0	115.0	115.0		2409	1.1	0.3	1	dbSNP_126	115	42,3140		2,38,1551	no	coding-synonymous	FHAD1	NM_052929.1		2,67,2214	AA,AG,GG		1.3199,2.0954,1.555		803/1413	15679393	71,4495	692	1591	2283	SO:0001819	synonymous_variant	114827	exon19			CATTGCGTACGAG	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.2409G>A	1.37:g.15679393G>A		86.0	0.0	0		85.0	33.0	0.388235	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		17	0.007783882783882784	6	0.012195121951219513	4	0.011049723756906077	1	0.0017482517482517483	6	0.0079155672823219	g	0.085	-1.176888	0.01646	0.020954	0.013199	ENSG00000142621	ENST00000444385	.	.	.	5.1	1.1	0.20463	.	.	.	.	.	T	0.16342	0.0393	.	.	.	0.30416	N	0.778556	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	4.2955	0.10899	0.1469:0.4642:0.3058:0.083	rs35368057	.	.	.	H	122	.	.	R	+	2	0	FHAD1	15551980	0.000000	0.05858	0.310000	0.25168	0.002000	0.02628	0.458000	0.21892	0.023000	0.15187	-2.364000	0.00238	CGT	G|0.991;A|0.009	0.009	strong		0.493	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
HIST1H2AK	8330	hgsc.bcm.edu	37	6	27805865	27805865	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27805865G>A	ENST00000330180.2	-	1	252	c.253C>T	c.(253-255)Cag>Tag	p.Q85*	HIST1H2BN_ENST00000606613.1_5'Flank|HIST1H2BN_ENST00000396980.3_5'Flank	NM_003510.2	NP_003501.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	85						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(2)|endometrium(2)|kidney(1)|lung(3)|upper_aerodigestive_tract(2)	10						ATGGCCAGCTGCAAGTGGCGC	0.632																																					p.Q85X		Atlas-SNP	.											.	HIST1H2AK	28	.	0			c.C253T						PASS	.						116.0	117.0	116.0					6																	27805865		2203	4298	6501	SO:0001587	stop_gained	8330	exon1			CCAGCTGCAAGTG	Z83739	CCDS4632.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000184348	ENSG00000275221		"""Histones / Replication-dependent"""	4726	protein-coding gene	gene with protein product		602788	"""H2A histone family, member D"", ""histone 1, H2ak"""	H2AFD		9439656, 12408966	Standard	NM_003510		Approved	H2A/d	uc003njs.3	P0C0S8	OTTHUMG00000016382	ENST00000330180.2:c.253C>T	6.37:g.27805865G>A	ENSP00000330307:p.Gln85*	121.0	0.0	0		128.0	50.0	0.390625	NM_003510	P02261|Q2M1R2|Q76PA6	Nonsense_Mutation	SNP	ENST00000330180.2	37	CCDS4632.1	.	.	.	.	.	.	.	.	.	.	.	28.7	4.945640	0.92593	.	.	ENSG00000184348	ENST00000330180	.	.	.	4.28	4.28	0.50868	.	0.000000	0.30168	U	0.010251	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.5671	0.84601	0.0:0.0:1.0:0.0	.	.	.	.	X	85	.	ENSP00000330307:Q85X	Q	-	1	0	HIST1H2AK	27913844	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.459000	0.97638	2.295000	0.77249	0.555000	0.69702	CAG	.	.	none		0.632	HIST1H2AK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043814.1	NM_003510	
SLC6A11	6538	hgsc.bcm.edu	37	3	10960057	10960057	+	Missense_Mutation	SNP	G	G	A	rs376135284		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:10960057G>A	ENST00000254488.2	+	8	1105	c.1039G>A	c.(1039-1041)Gtg>Atg	p.V347M		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	347					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	CACCAGCTTCGTGGCTGGGTT	0.597																																					p.V347M		Atlas-SNP	.											.	SLC6A11	87	.	0			c.G1039A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	120.0	95.0	103.0		1039	3.4	1.0	3		103	0,8600		0,0,4300	no	missense	SLC6A11	NM_014229.1	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	347/633	10960057	1,13005	2203	4300	6503	SO:0001583	missense	6538	exon8			AGCTTCGTGGCTG	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1039G>A	3.37:g.10960057G>A	ENSP00000254488:p.Val347Met	111.0	0.0	0		100.0	42.0	0.42	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	37	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470463	0.63625	2.27E-4	0.0	ENSG00000132164	ENST00000254488	T	0.74632	-0.86	4.29	3.41	0.39046	.	0.070049	0.56097	D	0.000028	T	0.75258	0.3825	M	0.66506	2.035	0.80722	D	1	P	0.42518	0.782	P	0.45195	0.473	T	0.77019	-0.2743	10	0.62326	D	0.03	.	12.3978	0.55395	0.0849:0.0:0.9151:0.0	.	347	P48066	S6A11_HUMAN	M	347	ENSP00000254488:V347M	ENSP00000254488:V347M	V	+	1	0	SLC6A11	10935057	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	4.372000	0.59530	0.926000	0.37118	0.484000	0.47621	GTG	.	.	weak		0.597	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
CFAP57	149465	hgsc.bcm.edu	37	1	43680952	43680952	+	Silent	SNP	C	C	T	rs74422853	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43680952C>T	ENST00000372492.4	+	12	2280	c.1956C>T	c.(1954-1956)ttC>ttT	p.F652F		NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		652										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ATGATCAGTTCCTGCTGACTG	0.542													C|||	128	0.0255591	0.0348	0.0029	5008	,	,		20606	0.0		0.008	False		,,,				2504	0.0736				p.F652F		Atlas-SNP	.											.	WDR65	76	.	0			c.C1956T						PASS	.																																			SO:0001819	synonymous_variant	149465	exon12			TCAGTTCCTGCTG																												ENST00000372492.4:c.1956C>T	1.37:g.43680952C>T		123.0	0.0	0		113.0	61.0	0.539823	NM_001195831	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				C|0.989;T|0.011	0.011	strong		0.542	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
FREM1	158326	hgsc.bcm.edu	37	9	14740229	14740229	+	Silent	SNP	G	G	A	rs187325866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:14740229G>A	ENST00000380880.3	-	36	7041	c.6258C>T	c.(6256-6258)taC>taT	p.Y2086Y	FREM1_ENST00000380894.1_Silent_p.Y622Y|FREM1_ENST00000422223.2_Silent_p.Y2086Y|FREM1_ENST00000380881.4_Silent_p.Y2087Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	2086	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GGTTGCCCAGGTATCTAAATG	0.413																																					p.Y2086Y		Atlas-SNP	.											.	FREM1	261	.	0			c.C6258T						PASS	.	G	,	6,3836		0,6,1915	87.0	85.0	85.0		1866,6258	3.5	0.5	9		85	14,8270		0,14,4128	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	0,20,6043	AA,AG,GG		0.169,0.1562,0.1649	,	622/716,2086/2180	14740229	20,12106	1921	4142	6063	SO:0001819	synonymous_variant	158326	exon37			GCCCAGGTATCTA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.6258C>T	9.37:g.14740229G>A		42.0	0.0	0		64.0	32.0	0.5	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.999;A|0.001	0.001	strong		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
CAPRIN2	65981	hgsc.bcm.edu	37	12	30881884	30881884	+	Missense_Mutation	SNP	G	G	A	rs374198235		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:30881884G>A	ENST00000395805.2	-	8	2027	c.1480C>T	c.(1480-1482)Cca>Tca	p.P494S	CAPRIN2_ENST00000298892.5_Missense_Mutation_p.P494S|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.P494S|CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.P161S|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.P494S	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					CACAGCTTTGGTGTCTCCTGT	0.468																																					p.P494S		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.C1480T						PASS	.						169.0	152.0	158.0					12																	30881884		2203	4300	6503	SO:0001583	missense	65981	exon8			GCTTTGGTGTCTC	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"""C1q domain containing 1"""	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.1480C>T	12.37:g.30881884G>A	ENSP00000379150:p.Pro494Ser	161.0	0.0	0		155.0	92.0	0.593548	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952458	0.34471	.	.	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000308433;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T;T	0.74315	2.51;-0.56;2.92;-0.54;-0.83;2.91;2.53	4.99	4.1	0.47936	.	0.266533	0.37219	N	0.002181	T	0.57066	0.2028	N	0.08118	0	0.33516	D	0.591802	B;P;B;B;B;B;B	0.39216	0.063;0.664;0.335;0.328;0.022;0.005;0.022	B;B;B;B;B;B;B	0.43018	0.013;0.405;0.058;0.085;0.005;0.008;0.005	T	0.66626	-0.5876	10	0.39692	T	0.17	-1.1961	8.8373	0.35119	0.2304:0.0:0.7696:0.0	.	494;220;494;494;494;494;494	Q6IMN6-6;E9PAU5;Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;.;.;CAPR2_HUMAN;.;.	S	240;494;494;494;161;494;220;413	ENSP00000415407:P240S;ENSP00000298892:P494S;ENSP00000379150:P494S;ENSP00000251071:P494S;ENSP00000309785:P161S;ENSP00000391479:P494S;ENSP00000438010:P413S	ENSP00000251071:P494S	P	-	1	0	CAPRIN2	30773151	0.278000	0.24230	1.000000	0.80357	0.979000	0.70002	0.934000	0.28910	1.225000	0.43566	0.561000	0.74099	CCA	.	.	alt		0.468	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925	
ZNF414	84330	hgsc.bcm.edu	37	19	8576390	8576390	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8576390C>T	ENST00000255616.8	-	6	1006	c.905G>A	c.(904-906)gGc>gAc	p.G302D	ZNF414_ENST00000393927.4_Missense_Mutation_p.G302D	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						GTCGGAGCCGCCCTGGGGTCT	0.706																																					p.G302D		Atlas-SNP	.											.	ZNF414	25	.	0			c.G905A						PASS	.						18.0	24.0	22.0					19																	8576390		2197	4295	6492	SO:0001583	missense	84330	exon6			GAGCCGCCCTGGG	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.905G>A	19.37:g.8576390C>T	ENSP00000255616:p.Gly302Asp	100.0	0.0	0		103.0	57.0	0.553398	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266899	0.80469	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.14766	2.48;2.48	4.53	4.53	0.55603	.	0.000000	0.52532	D	0.000080	T	0.25717	0.0626	L	0.29908	0.895	0.37759	D	0.926255	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.924	T	0.09185	-1.0686	10	0.72032	D	0.01	-19.322	14.3348	0.66581	0.0:1.0:0.0:0.0	.	302;302	Q96IQ9;A8MY94	ZN414_HUMAN;.	D	302	ENSP00000377504:G302D;ENSP00000255616:G302D	ENSP00000255616:G302D	G	-	2	0	ZNF414	8482390	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.815000	0.48018	2.231000	0.72958	0.313000	0.20887	GGC	.	.	none		0.706	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
DACT1	51339	hgsc.bcm.edu	37	14	59113721	59113721	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:59113721C>G	ENST00000335867.4	+	4	2404	c.2380C>G	c.(2380-2382)Caa>Gaa	p.Q794E	DACT1_ENST00000395153.3_Missense_Mutation_p.Q757E|DACT1_ENST00000556859.1_Missense_Mutation_p.Q513E|DACT1_ENST00000541264.2_Missense_Mutation_p.Q513E			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	794					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						TCTGCCCATTCAAACGGTAAC	0.532																																					p.Q794E		Atlas-SNP	.											.	DACT1	119	.	0			c.C2380G						PASS	.						98.0	102.0	101.0					14																	59113721		2203	4300	6503	SO:0001583	missense	51339	exon4			CCCATTCAAACGG	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2380C>G	14.37:g.59113721C>G	ENSP00000337439:p.Gln794Glu	50.0	0.0	0		30.0	13.0	0.433333	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.728843	0.48833	.	.	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	5.65	5.65	0.86999	.	0.268108	0.36778	N	0.002414	T	0.46132	0.1377	M	0.62723	1.935	0.50813	D	0.999891	B;B	0.33549	0.417;0.417	B;B	0.35971	0.215;0.215	T	0.27331	-1.0077	10	0.26408	T	0.33	-9.8241	19.9142	0.97043	0.0:1.0:0.0:0.0	.	757;794	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	E	513;513;757;794;513	ENSP00000451598:Q513E;ENSP00000378581:Q513E;ENSP00000378582:Q757E;ENSP00000337439:Q794E;ENSP00000442850:Q513E	ENSP00000337439:Q794E	Q	+	1	0	DACT1	58183474	0.628000	0.27138	0.094000	0.20943	0.591000	0.36615	2.362000	0.44169	2.941000	0.99782	0.655000	0.94253	CAA	.	.	none		0.532	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
NUTM2G	441457	hgsc.bcm.edu	37	9	99701002	99701002	+	Silent	SNP	C	C	T	rs199656301	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:99701002C>T	ENST00000372322.3	+	7	1818	c.1797C>T	c.(1795-1797)ctC>ctT	p.L599L	HIATL2_ENST00000506067.1_Intron|NUTM2G_ENST00000354649.3_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	599																	CCTTGGGTCTCCCTGGAGAGT	0.637																																					p.L599L		Atlas-SNP	.											.	FAM22G	66	.	0			c.C1797T						PASS	.						9.0	14.0	12.0					9																	99701002		685	1576	2261	SO:0001819	synonymous_variant	441457	exon7			GGGTCTCCCTGGA		CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member G"""	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1797C>T	9.37:g.99701002C>T		315.0	0.0	0		360.0	124.0	0.344444	NM_001170741	A6NNI5|Q5VZR3	Silent	SNP	ENST00000372322.3	37	CCDS55329.1																																																																																			T|1.000;|0.000	1.000	weak		0.637	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741	
DAO	1610	hgsc.bcm.edu	37	12	109293183	109293183	+	Missense_Mutation	SNP	T	T	G	rs113854555		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109293183T>G	ENST00000228476.3	+	10	1048	c.844T>G	c.(844-846)Ttc>Gtc	p.F282V	DAO_ENST00000551281.1_Missense_Mutation_p.F216V	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	282					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	ACGAACTGGCTTCCGGCCAGT	0.463																																					p.F282V		Atlas-SNP	.											.	DAO	58	.	0			c.T844G						PASS	.						38.0	34.0	35.0					12																	109293183		2203	4300	6503	SO:0001583	missense	1610	exon10			ACTGGCTTCCGGC	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.844T>G	12.37:g.109293183T>G	ENSP00000228476:p.Phe282Val	33.0	0.0	0		52.0	14.0	0.269231	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	t	9.649	1.141129	0.21205	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	T;T;T	0.80393	-1.37;-1.37;-1.37	5.14	2.72	0.32119	FAD dependent oxidoreductase (1);	0.163309	0.56097	D	0.000036	T	0.76615	0.4012	M	0.65975	2.015	0.31918	N	0.613876	B;B	0.14438	0.01;0.004	B;B	0.26202	0.067;0.028	T	0.73861	-0.3849	10	0.66056	D	0.02	-29.9761	6.7285	0.23371	0.0:0.2961:0.0:0.7039	.	282;265	P14920;Q7Z312	OXDA_HUMAN;.	V	216;282;159	ENSP00000446853:F216V;ENSP00000228476:F282V;ENSP00000449967:F159V	ENSP00000228476:F282V	F	+	1	0	DAO	107817312	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	1.774000	0.38573	0.280000	0.22209	-0.474000	0.04947	TTC	T|0.500;C|0.500	.	alt		0.463	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1		
CFAP46	54777	hgsc.bcm.edu	37	10	134664628	134664628	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134664628A>G	ENST00000368586.5	-	40	5856	c.5756T>C	c.(5755-5757)gTc>gCc	p.V1919A	TTC40_ENST00000263170.5_Missense_Mutation_p.V80A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TACCAGGCCGACGGAAGTGTA	0.632																																					p.V1919A		Atlas-SNP	.											.	TTC40	100	.	0			c.T5756C						PASS	.						75.0	73.0	74.0					10																	134664628		2203	4300	6503	SO:0001583	missense	54777	exon40			AGGCCGACGGAAG																												ENST00000368586.5:c.5756T>C	10.37:g.134664628A>G	ENSP00000357575:p.Val1919Ala	43.0	0.0	0		43.0	12.0	0.27907	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.621397	0.28889	.	.	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.13538	2.79;2.58	4.26	-0.92	0.10475	.	2.776180	0.01828	N	0.034516	T	0.14614	0.0353	L	0.50333	1.59	0.09310	N	1	B	0.22683	0.073	B	0.21917	0.037	T	0.32771	-0.9894	10	0.66056	D	0.02	.	4.4777	0.11752	0.5743:0.1622:0.2635:0.0	.	80	Q8IYW2	CJ092_HUMAN	A	1919;80	ENSP00000357575:V1919A;ENSP00000263170:V80A	ENSP00000263170:V80A	V	-	2	0	C10orf93	134514618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.025000	0.12413	-0.355000	0.08199	-0.290000	0.09829	GTC	.	.	none		0.632	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KIAA1033	23325	hgsc.bcm.edu	37	12	105550565	105550565	+	Silent	SNP	C	C	T	rs35149056	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:105550565C>T	ENST00000332180.5	+	27	2907	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						GCAGCAATGCCATTAGGTATG	0.308													C|||	217	0.0433307	0.0166	0.0692	5008	,	,		14135	0.001		0.0795	False		,,,				2504	0.0675				p.A940A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2820T						PASS	.	C		82,3618		1,80,1769	208.0	186.0	193.0		2820	4.9	1.0	12	dbSNP_126	193	613,7575		27,559,3508	no	coding-synonymous	KIAA1033	NM_015275.1		28,639,5277	TT,TC,CC		7.4866,2.2162,5.8462		940/1174	105550565	695,11193	1850	4094	5944	SO:0001819	synonymous_variant	23325	exon27			CAATGCCATTAGG	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2820C>T	12.37:g.105550565C>T		71.0	0.0	0		86.0	38.0	0.44186	NM_015275		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			C|0.946;T|0.054	0.054	strong		0.308	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
TIAM2	26230	hgsc.bcm.edu	37	6	155575639	155575639	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155575639C>T	ENST00000461783.3	+	28	5673	c.4400C>T	c.(4399-4401)cCa>cTa	p.P1467L	TIAM2_ENST00000360366.4_Missense_Mutation_p.P1491L|TIAM2_ENST00000275246.7_Missense_Mutation_p.P392L|TIAM2_ENST00000318981.5_Missense_Mutation_p.P1467L|TIAM2_ENST00000529824.2_Missense_Mutation_p.P1496L|TIAM2_ENST00000456144.1_Missense_Mutation_p.P1496L|TIAM2_ENST00000367174.2_Missense_Mutation_p.P843L|TIAM2_ENST00000456877.2_Missense_Mutation_p.P779L|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000528391.2_Missense_Mutation_p.P803L			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1467	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TGTGAATTACCACTGGAGAAA	0.448																																					p.P1467L		Atlas-SNP	.											TIAM2,NS,carcinoma,+1,1	TIAM2	161	1	0			c.C4400T						PASS	.						163.0	143.0	150.0					6																	155575639		2203	4300	6503	SO:0001583	missense	26230	exon25			AATTACCACTGGA		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4400C>T	6.37:g.155575639C>T	ENSP00000437188:p.Pro1467Leu	144.0	0.0	0		175.0	94.0	0.537143	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415307	0.83449	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	T;T;T;T;T;T;T;T;T	0.09445	3.44;3.18;3.44;3.21;3.38;3.18;3.23;3.31;2.98	5.66	5.66	0.87406	.	0.121042	0.56097	D	0.000030	T	0.11965	0.0291	L	0.36672	1.1	0.50632	D	0.999885	P;D;D;D	0.57899	0.885;0.981;0.981;0.967	P;P;P;P	0.54629	0.546;0.757;0.757;0.576	T	0.02339	-1.1174	10	0.41790	T	0.15	.	17.934	0.89007	0.0:1.0:0.0:0.0	.	803;1496;1491;1467	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	L	1467;1713;1496;1467;843;1491;1496;779;803;392	ENSP00000437188:P1467L;ENSP00000407746:P1496L;ENSP00000327315:P1467L;ENSP00000356142:P843L;ENSP00000353528:P1491L;ENSP00000433348:P1496L;ENSP00000407183:P779L;ENSP00000435335:P803L;ENSP00000275246:P392L	ENSP00000275246:P392L	P	+	2	0	TIAM2	155617331	0.980000	0.34600	0.351000	0.25721	0.997000	0.91878	5.249000	0.65427	2.673000	0.90976	0.650000	0.86243	CCA	.	.	none		0.448	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48143315	48143315	+	Missense_Mutation	SNP	A	A	G	rs145878042	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48143315A>G	ENST00000449771.2	-	10	987	c.899T>C	c.(898-900)cTg>cCg	p.L300P	RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L258P|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L258P|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L258P|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L258P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	300					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GGTGGTCACCAGCCCCTGCAG	0.637													A|||	9	0.00179712	0.0	0.0029	5008	,	,		8210	0.0		0.007	False		,,,				2504	0.0				p.L300P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T899C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	5,4401	9.9+/-24.2	0,5,2198	50.0	44.0	46.0		899,773,773	4.3	1.0	12	dbSNP_134	46	105,8495	56.4+/-117.6	2,101,4197	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	98,98,98	2,106,6395	GG,GA,AA		1.2209,0.1135,0.8458	probably-damaging,probably-damaging,probably-damaging	300/924,258/882,258/882	48143315	110,12896	2203	4300	6503	SO:0001583	missense	10411	exon10			GTCACCAGCCCCT	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.899T>C	12.37:g.48143315A>G	ENSP00000395708:p.Leu300Pro	20.0	0.0	0		14.0	5.0	0.357143	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	A	21.4	4.141017	0.77775	0.001135	0.012209	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	D;D;D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04;-3.04;-3.04	4.28	4.28	0.50868	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.094510	0.45126	D	0.000383	D	0.89705	0.6792	N	0.21508	0.67	0.80722	D	1	B;D;D	0.76494	0.382;0.999;0.999	P;D;D	0.74674	0.448;0.962;0.984	D	0.91472	0.5197	10	0.87932	D	0	.	12.7023	0.57041	1.0:0.0:0.0:0.0	.	312;300;300	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	P	258;300;258;258;258;300;312;258;300	ENSP00000384521:L258P;ENSP00000395708:L300P;ENSP00000448619:L258P;ENSP00000171000:L258P;ENSP00000373864:L300P;ENSP00000448480:L258P;ENSP00000378764:L300P	ENSP00000171000:L258P	L	-	2	0	RAPGEF3	46429582	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.635000	0.91006	1.941000	0.56285	0.528000	0.53228	CTG	A|0.993;G|0.007	0.007	strong		0.637	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
BTBD8	284697	hgsc.bcm.edu	37	1	92568089	92568089	+	Missense_Mutation	SNP	A	A	G	rs17131602	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:92568089A>G	ENST00000342818.3	+	3	643	c.407A>G	c.(406-408)aAg>aGg	p.K136R	BTBD8_ENST00000370382.3_Missense_Mutation_p.K136R|BTBD8_ENST00000540648.1_Missense_Mutation_p.K136R	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	136			K -> R (in dbSNP:rs17131602).			nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		CTTAGGAAAAAGATAATGGAG	0.284													A|||	28	0.00559105	0.0015	0.0086	5008	,	,		14566	0.0		0.0189	False		,,,				2504	0.001				p.K136R		Atlas-SNP	.											BTBD8,colon,carcinoma,0,4	BTBD8	32	4	0			c.A407G						PASS	.	A	ARG/LYS	14,4392	12.9+/-30.5	0,14,2189	57.0	58.0	58.0		407	3.2	0.7	1	dbSNP_123	58	146,8452	50.6+/-110.7	3,140,4156	yes	missense	BTBD8	NM_183242.3	26	3,154,6345	GG,GA,AA		1.6981,0.3177,1.2304	possibly-damaging	136/379	92568089	160,12844	2203	4299	6502	SO:0001583	missense	284697	exon3			GGAAAAAGATAAT	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.407A>G	1.37:g.92568089A>G	ENSP00000343686:p.Lys136Arg	188.0	0.0	0		145.0	66.0	0.455172	NM_183242	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	37	CCDS737.1	20	0.009157509157509158	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	A	11.82	1.752559	0.31046	0.003177	0.016981	ENSG00000189195	ENST00000370382;ENST00000342818;ENST00000540648	T;T;T	0.65364	1.86;-0.15;1.85	5.66	3.2	0.36748	BTB/POZ-like (1);BTB/POZ fold (1);	0.279011	0.30584	N	0.009314	T	0.32645	0.0836	L	0.55481	1.735	0.18873	N	0.999988	P	0.35226	0.491	B	0.37015	0.239	T	0.17289	-1.0374	10	0.14252	T	0.57	-5.708	8.3692	0.32404	0.6129:0.0:0.0:0.3871	rs17131602;rs52812935;rs17131602	136	Q5XKL5	BTBD8_HUMAN	R	136	ENSP00000359408:K136R;ENSP00000343686:K136R;ENSP00000443397:K136R	ENSP00000343686:K136R	K	+	2	0	BTBD8	92340677	1.000000	0.71417	0.720000	0.30636	0.622000	0.37654	1.661000	0.37408	0.953000	0.37825	0.482000	0.46254	AAG	A|0.986;G|0.014	0.014	strong		0.284	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	
PMS2	5395	hgsc.bcm.edu	37	7	6018231	6018231	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6018231T>C	ENST00000265849.7	-	13	2376	c.2271A>G	c.(2269-2271)gaA>gaG	p.E757E	PMS2_ENST00000406569.3_Intron|PMS2_ENST00000382321.4_Silent_p.E356E|PMS2_ENST00000441476.2_Silent_p.E651E	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	757					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		ACTTACCATTTTCATCGATAA	0.433			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.E757E		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.A2271G						PASS	.						78.0	64.0	69.0					7																	6018231		2194	4281	6475	SO:0001819	synonymous_variant	5395	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	ACCATTTTCATCG		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2271A>G	7.37:g.6018231T>C		325.0	0.0	0		396.0	212.0	0.535354	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																			.	.	none		0.433	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
SGK1	6446	hgsc.bcm.edu	37	6	134495709	134495709	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495709C>T	ENST00000237305.7	-	2	180	c.92G>A	c.(91-93)aGg>aAg	p.R31K	SGK1_ENST00000528577.1_Missense_Mutation_p.R59K|SGK1_ENST00000413996.3_Missense_Mutation_p.R45K|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.R21K|SGK1_ENST00000475719.2_Missense_Mutation_p.R31K|SGK1_ENST00000367858.5_Missense_Mutation_p.R126K	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	31	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		ACCCATCCTCCTCTGCTTCAT	0.428											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R126K		Atlas-SNP	.											SGK1_ENST00000367858,NS,lymphoid_neoplasm,-1,2	SGK1	387	2	0			c.G377A						PASS	.						78.0	78.0	78.0					6																	134495709		2203	4300	6503	SO:0001583	missense	6446	exon4			ATCCTCCTCTGCT	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.92G>A	6.37:g.134495709C>T	ENSP00000237305:p.Arg31Lys	70.0	0.0	0	1611	40.0	8.0	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.971432	0.92919	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	L	0.49455	1.56	0.80722	D	1	B;B;B;B;B;B	0.33694	0.282;0.009;0.05;0.106;0.421;0.05	B;B;B;B;B;B	0.37346	0.205;0.009;0.115;0.149;0.247;0.043	T	0.50457	-0.8826	10	0.48119	T	0.1	.	20.2576	0.98430	0.0:1.0:0.0:0.0	.	59;45;31;21;126;31	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	K	126;45;31;21;59;31;95	ENSP00000356832:R126K;ENSP00000396242:R45K;ENSP00000237305:R31K;ENSP00000356831:R21K;ENSP00000434450:R59K;ENSP00000434302:R31K;ENSP00000435577:R95K	ENSP00000237305:R31K	R	-	2	0	SGK1	134537402	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.818000	0.86416	2.783000	0.95769	0.655000	0.94253	AGG	.	.	none		0.428	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
BTD	686	hgsc.bcm.edu	37	3	15686611	15686611	+	Silent	SNP	C	C	T	rs397514404|rs397514435|rs372039874	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:15686611C>T	ENST00000303498.5	+	4	1357	c.1248C>T	c.(1246-1248)caC>caT	p.H416H	BTD_ENST00000437172.1_Silent_p.H418H|BTD_ENST00000449107.1_Silent_p.H418H|BTD_ENST00000383778.4_Silent_p.H396H	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	416					biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						GCTATCTCCACGTCTGTTCCA	0.502													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		20372	0.0		0.0	False		,,,				2504	0.0				p.H416H		Atlas-SNP	.											.	BTD	49	.	0			c.C1248T						PASS	.	C		0,4406		0,0,2203	158.0	152.0	154.0		1248	-11.2	0.0	3		154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BTD	NM_000060.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		416/544	15686611	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	686	exon4			TCTCCACGTCTGT	AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1248C>T	3.37:g.15686611C>T		117.0	0.0	0		131.0	64.0	0.48855	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Silent	SNP	ENST00000303498.5	37	CCDS2628.1																																																																																			.	.	weak		0.502	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060	
SORCS1	114815	hgsc.bcm.edu	37	10	108434858	108434858	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:108434858A>C	ENST00000263054.6	-	14	1896	c.1889T>G	c.(1888-1890)cTt>cGt	p.L630R	SORCS1_ENST00000369698.1_Missense_Mutation_p.L165R|SORCS1_ENST00000344440.6_Missense_Mutation_p.L630R	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	630					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ATCCACAAAAAGTGGAATAGA	0.388																																					p.L630R		Atlas-SNP	.											.	SORCS1	534	.	0			c.T1889G						PASS	.						124.0	118.0	120.0					10																	108434858		2203	4300	6503	SO:0001583	missense	114815	exon14			ACAAAAAGTGGAA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.1889T>G	10.37:g.108434858A>C	ENSP00000263054:p.Leu630Arg	66.0	0.0	0		74.0	25.0	0.337838	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488184	0.84854	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.33438	1.41;1.41;1.41	5.92	5.92	0.95590	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.61198	0.2328	M	0.86178	2.8	0.51767	D	0.999937	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0	T	0.65833	-0.6072	9	.	.	.	-15.917	16.3631	0.83280	1.0:0.0:0.0:0.0	.	630;630;630;630;630	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	R	165;630;630	ENSP00000358712:L165R;ENSP00000263054:L630R;ENSP00000345964:L630R	.	L	-	2	0	SORCS1	108424848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.266000	0.75297	0.533000	0.62120	CTT	.	.	none		0.388	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907263	12907263	+	Nonstop_Mutation	SNP	A	A	T	rs370005849		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907263A>T	ENST00000317869.6	-	2	1105	c.880T>A	c.(880-882)Taa>Aaa	p.*294K		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	0						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CTATGTGCTTAAGAGTCATCC	0.448																																					p.X294K		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.T880A						PASS	.	A	LYS/stop	0,4406		0,0,2203	113.0	124.0	120.0		880	-0.2	0.0	1		120	2,8596		0,2,4297	no	stop-lost	HNRNPCL1	NM_001013631.1		0,2,6500	TT,TA,AA		0.0233,0.0,0.0154		294/294	12907263	2,13002	2203	4299	6502	SO:0001578	stop_lost	343069	exon2			GTGCTTAAGAGTC	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.880T>A	1.37:g.12907263A>T		126.0	0.0	0		130.0	30.0	0.230769	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.569	-0.841782	0.02671	0.0	2.33E-4	ENSG00000179172	ENST00000317869	.	.	.	1.09	-0.244	0.13031	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6398	0.17557	0.7289:0.271:0.0:0.0	.	.	.	.	K	294	.	.	X	-	1	0	HNRNPCL1	12829850	1.000000	0.71417	0.023000	0.16930	0.082000	0.17680	1.836000	0.39191	-0.137000	0.11455	-1.850000	0.00570	TAA	.	.	none		0.448	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
KRT7	3855	hgsc.bcm.edu	37	12	52636919	52636919	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52636919C>T	ENST00000331817.5	+	6	1165	c.982C>T	c.(982-984)Cag>Tag	p.Q328*	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	328	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	CATCAAGAACCAGGTGGGACA	0.587																																					p.Q328X		Atlas-SNP	.											.	KRT7	48	.	0			c.C982T						PASS	.						75.0	63.0	67.0					12																	52636919		2203	4300	6503	SO:0001587	stop_gained	3855	exon6			AAGAACCAGGTGG		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.982C>T	12.37:g.52636919C>T	ENSP00000329243:p.Gln328*	37.0	0.0	0		40.0	8.0	0.2	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Nonsense_Mutation	SNP	ENST00000331817.5	37	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	C	37	6.293061	0.97449	.	.	ENSG00000135480	ENST00000331817;ENST00000422319;ENST00000551537	.	.	.	3.84	3.84	0.44239	.	0.000000	0.35805	N	0.002977	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.3259	0.82979	0.0:1.0:0.0:0.0	.	.	.	.	X	328;304;328	.	ENSP00000329243:Q328X	Q	+	1	0	KRT7	50923186	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.609000	0.82925	2.160000	0.67779	0.561000	0.74099	CAG	.	.	none		0.587	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
GATM	2628	hgsc.bcm.edu	37	15	45660421	45660421	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45660421A>G	ENST00000396659.3	-	4	861	c.522T>C	c.(520-522)gtT>gtC	p.V174V	GATM_ENST00000558336.1_Silent_p.V174V	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	174					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	CATTGCCCACAACTATCAGGA	0.448																																					p.V174V		Atlas-SNP	.											.	GATM	34	.	0			c.T522C						PASS	.						111.0	95.0	100.0					15																	45660421		2198	4298	6496	SO:0001819	synonymous_variant	2628	exon4			GCCCACAACTATC	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.522T>C	15.37:g.45660421A>G		98.0	0.0	0		54.0	23.0	0.425926	NM_001482	B4DH99|B4DPI3|Q53EQ4	Silent	SNP	ENST00000396659.3	37	CCDS10122.1																																																																																			.	.	none		0.448	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482	
SFTPA1	653509	hgsc.bcm.edu	37	10	81373562	81373562	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:81373562C>G	ENST00000398636.3	+	6	578	c.440C>G	c.(439-441)aCt>aGt	p.T147S	SFTPA1_ENST00000372313.5_Missense_Mutation_p.T88S|SFTPA1_ENST00000372308.3_Missense_Mutation_p.T147S|SFTPA1_ENST00000419470.2_Missense_Mutation_p.T162S|SFTPA1_ENST00000428376.2_Missense_Mutation_p.T147S	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1	147	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				lipid transport (GO:0006869)|respiratory gaseous exchange (GO:0007585)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|lipid transporter activity (GO:0005319)			endometrium(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			CAGTCCATCACTTTTGATGCC	0.552																																					p.T162S		Atlas-SNP	.											.	SFTPA1	23	.	0			c.C485G						PASS	.						57.0	61.0	59.0					10																	81373562		2191	4249	6440	SO:0001583	missense	653509	exon6			CCATCACTTTTGA	BC026229	CCDS44444.1, CCDS44445.1, CCDS44444.2	10q22.3	2012-11-02	2008-08-26			ENSG00000122852		"""Collectins"""	10798	protein-coding gene	gene with protein product	"""surfactant, pulmonary-associated protein A1A"""	178630	"""surfactant, pulmonary-associated protein A1"""	SFTP1			Standard	NM_001093770		Approved	SP-A, SP-A1, COLEC4	uc009xry.3	Q8IWL2		ENST00000398636.3:c.440C>G	10.37:g.81373562C>G	ENSP00000381633:p.Thr147Ser	306.0	0.0	0		299.0	115.0	0.384615	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Missense_Mutation	SNP	ENST00000398636.3	37	CCDS44445.1	.	.	.	.	.	.	.	.	.	.	.	0.102	-1.150419	0.01700	.	.	ENSG00000122852	ENST00000372308;ENST00000398636;ENST00000428376;ENST00000372313;ENST00000419470;ENST00000394569;ENST00000429958;ENST00000439264	T;T;T;T;T;D;D	0.88201	0.31;0.31;0.31;0.31;0.31;-2.35;-2.35	2.6	0.155	0.14906	C-type lectin fold (2);C-type lectin-like (2);C-type lectin (6);	0.446637	0.24189	N	0.040729	T	0.76898	0.4052	L	0.28776	0.89	0.09310	N	0.999992	B;B;B	0.31153	0.202;0.168;0.31	B;B;B	0.33846	0.171;0.069;0.171	T	0.62120	-0.6921	10	0.12103	T	0.63	-0.5574	4.1587	0.10273	0.6468:0.2212:0.1321:0.0	.	147;162;147	Q8IWL1;G5E9J3;Q8IWL2	SFPA2_HUMAN;.;SFTA1_HUMAN	S	147;147;147;88;162;147;147;147	ENSP00000361382:T147S;ENSP00000381633:T147S;ENSP00000411102:T147S;ENSP00000361387:T88S;ENSP00000397082:T162S;ENSP00000395527:T147S;ENSP00000401649:T147S	ENSP00000361382:T147S	T	+	2	0	SFTPA1	81043568	0.363000	0.24989	0.207000	0.23584	0.043000	0.13939	1.187000	0.32090	0.016000	0.14998	0.297000	0.19635	ACT	.	.	none		0.552	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411	
MYH10	4628	hgsc.bcm.edu	37	17	8402769	8402769	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8402769T>G	ENST00000269243.4	-	28	3815	c.3677A>C	c.(3676-3678)aAg>aCg	p.K1226T	MYH10_ENST00000379980.4_Missense_Mutation_p.K1242T|MYH10_ENST00000360416.3_Missense_Mutation_p.K1257T|MYH10_ENST00000396239.1_Missense_Mutation_p.K1247T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1226					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CAGGCCCTGCTTGTTCTTCTC	0.473																																					p.K1257T		Atlas-SNP	.											.	MYH10	148	.	0			c.A3770C						PASS	.						108.0	103.0	105.0					17																	8402769		2203	4300	6503	SO:0001583	missense	4628	exon30			CCCTGCTTGTTCT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.3677A>C	17.37:g.8402769T>G	ENSP00000269243:p.Lys1226Thr	160.0	0.0	0		154.0	50.0	0.324675	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190916	0.78789	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	5.03	5.03	0.67393	Myosin tail (1);	0.106621	0.64402	D	0.000005	D	0.92358	0.7575	M	0.83692	2.655	0.54753	D	0.999986	D;D;D	0.55605	0.972;0.965;0.972	D;D;D	0.70227	0.968;0.945;0.968	D	0.93517	0.6858	10	0.87932	D	0	.	14.9308	0.70914	0.0:0.0:0.0:1.0	.	1235;1257;1226	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	T	1226;1257;1247;1242	ENSP00000269243:K1226T;ENSP00000353590:K1257T;ENSP00000379539:K1247T;ENSP00000369315:K1242T	ENSP00000269243:K1226T	K	-	2	0	MYH10	8343494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.961000	0.63681	2.114000	0.64651	0.533000	0.62120	AAG	.	.	none		0.473	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
SLC2A9	56606	hgsc.bcm.edu	37	4	9998476	9998476	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:9998476A>G	ENST00000264784.3	-	3	392	c.339T>C	c.(337-339)acT>acC	p.T113T	SLC2A9_ENST00000506583.1_Silent_p.T84T|SLC2A9_ENST00000309065.3_Silent_p.T84T	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	113					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	ATATGGACACAGTCACAGACC	0.473																																					p.T113T		Atlas-SNP	.											.	SLC2A9	158	.	0			c.T339C						PASS	.						144.0	124.0	131.0					4																	9998476		2203	4300	6503	SO:0001819	synonymous_variant	56606	exon3			GGACACAGTCACA	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.339T>C	4.37:g.9998476A>G		216.0	0.0	0		203.0	60.0	0.295566	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	37	CCDS3407.1																																																																																			.	.	none		0.473	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
PAPLN	89932	hgsc.bcm.edu	37	14	73718474	73718474	+	Missense_Mutation	SNP	G	G	T	rs141960540	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:73718474G>T	ENST00000554301.1	+	8	936	c.773G>T	c.(772-774)gGt>gTt	p.G258V	PAPLN_ENST00000427855.1_Missense_Mutation_p.G258V|PAPLN_ENST00000381166.3_Missense_Mutation_p.G258V|PAPLN_ENST00000340738.5_Missense_Mutation_p.G231V|PAPLN_ENST00000555445.1_Missense_Mutation_p.G258V			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	258						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TACGAGCGGGGTGCTGAGGGG	0.662													G|||	5	0.000998403	0.0008	0.0029	5008	,	,		16188	0.0		0.002	False		,,,				2504	0.0				p.G231V		Atlas-SNP	.											.	PAPLN	180	.	0			c.G692T						PASS	.	G	VAL/GLY	8,4394		0,8,2193	24.0	30.0	28.0		692	4.8	0.7	14	dbSNP_134	28	18,8576		0,18,4279	no	missense	PAPLN	NM_173462.3	109	0,26,6472	TT,TG,GG		0.2094,0.1817,0.2001	probably-damaging	231/1252	73718474	26,12970	2201	4297	6498	SO:0001583	missense	89932	exon8			AGCGGGGTGCTGA	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.773G>T	14.37:g.73718474G>T	ENSP00000451803:p.Gly258Val	122.0	0.0	0		146.0	76.0	0.520548	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	19.70	3.876857	0.72180	0.001817	0.002094	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	4.77	4.77	0.60923	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.56262	0.1973	L	0.38531	1.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.73380	0.967;0.98;0.959	T	0.53012	-0.8498	9	0.34782	T	0.22	.	13.2075	0.59805	0.0:0.1601:0.8398:0.0	.	258;258;231	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	V	231;258;258;258;258	ENSP00000345395:G231V;ENSP00000403403:G258V;ENSP00000370558:G258V;ENSP00000451803:G258V;ENSP00000451729:G258V	ENSP00000216658:G258V	G	+	2	0	PAPLN	72788227	1.000000	0.71417	0.707000	0.30419	0.682000	0.39822	6.561000	0.73955	2.179000	0.69175	0.561000	0.74099	GGT	G|0.998;T|0.002	0.002	strong		0.662	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
ROR2	4920	hgsc.bcm.edu	37	9	94495595	94495595	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:94495595C>T	ENST00000375708.3	-	6	944	c.746G>A	c.(745-747)cGt>cAt	p.R249H	ROR2_ENST00000375715.1_Missense_Mutation_p.R109H|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	249	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCACAGCTCACGCGGCTTGGG	0.647																																					p.R249H		Atlas-SNP	.											.	ROR2	167	.	0			c.G746A						PASS	.						44.0	41.0	42.0					9																	94495595		2203	4299	6502	SO:0001583	missense	4920	exon6			AGCTCACGCGGCT	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.746G>A	9.37:g.94495595C>T	ENSP00000364860:p.Arg249His	96.0	0.0	0		101.0	8.0	0.0792079	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	35	5.489687	0.96323	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.76060	0.54;-0.99	4.37	4.37	0.52481	Frizzled domain (2);Kringle (1);	0.000000	0.39146	N	0.001446	D	0.83830	0.5339	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	0.977;1.0;0.973	P;D;P	0.87578	0.581;0.998;0.763	D	0.85333	0.1091	10	0.56958	D	0.05	.	17.1327	0.86730	0.0:1.0:0.0:0.0	.	249;249;109	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	H	109;249	ENSP00000364867:R109H;ENSP00000364860:R249H	ENSP00000364860:R249H	R	-	2	0	ROR2	93535416	1.000000	0.71417	0.978000	0.43139	0.949000	0.60115	7.560000	0.82277	2.271000	0.75665	0.511000	0.50034	CGT	.	.	none		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
ZNF561	93134	hgsc.bcm.edu	37	19	9721218	9721218	+	Silent	SNP	G	G	A	rs138137635		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9721218G>A	ENST00000302851.3	-	6	1482	c.1119C>T	c.(1117-1119)gcC>gcT	p.A373A	ZNF561_ENST00000354661.4_Silent_p.A237A|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000424629.1_Silent_p.A304A|ZNF561_ENST00000495503.1_5'Flank	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	373					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						ATGTAGTGAAGGCTTTCCCAC	0.438													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21339	0.0		0.0	False		,,,				2504	0.0				p.A373A		Atlas-SNP	.											.	ZNF561	64	.	0			c.C1119T						PASS	.	G		0,4406		0,0,2203	124.0	116.0	119.0		1119	-0.2	0.0	19	dbSNP_134	119	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	ZNF561	NM_152289.2		0,11,6492	AA,AG,GG		0.1279,0.0,0.0846		373/487	9721218	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	93134	exon6			AGTGAAGGCTTTC	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"""Zinc fingers, C2H2-type"", ""-"""	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.1119C>T	19.37:g.9721218G>A		57.0	0.0	0		61.0	33.0	0.540984	NM_152289	B4E2Q8|Q6PJS0	Silent	SNP	ENST00000302851.3	37	CCDS12216.2																																																																																			G|0.999;A|0.001	0.001	strong		0.438	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289	
PCDH17	27253	hgsc.bcm.edu	37	13	58208047	58208047	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:58208047A>C	ENST00000377918.3	+	1	1393	c.1367A>C	c.(1366-1368)aAg>aCg	p.K456T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	456	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		AACTCCACCAAGTCGTTCGCG	0.607																																					p.K456T	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											PCDH17,colon,carcinoma,-1,1	PCDH17	304	1	0			c.A1367C						PASS	.						53.0	43.0	46.0					13																	58208047		2202	4300	6502	SO:0001583	missense	27253	exon1			CCACCAAGTCGTT	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1367A>C	13.37:g.58208047A>C	ENSP00000367151:p.Lys456Thr	47.0	0.0	0		63.0	10.0	0.15873	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.309656	0.60414	.	.	ENSG00000118946	ENST00000377918	T	0.42131	0.98	5.58	5.58	0.84498	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.54255	0.1847	L	0.35644	1.08	0.50813	D	0.999899	D;D	0.76494	0.997;0.999	D;D	0.77557	0.959;0.99	T	0.50550	-0.8815	9	.	.	.	.	15.7465	0.77949	1.0:0.0:0.0:0.0	.	456;456	O14917-2;O14917	.;PCD17_HUMAN	T	456	ENSP00000367151:K456T	.	K	+	2	0	PCDH17	57106048	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.133000	0.65898	0.459000	0.35465	AAG	.	.	none		0.607	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
KIAA0232	9778	hgsc.bcm.edu	37	4	6843852	6843852	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:6843852A>G	ENST00000307659.5	+	4	745	c.290A>G	c.(289-291)aAg>aGg	p.K97R	KIAA0232_ENST00000425103.1_Missense_Mutation_p.K97R	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	97							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						GGAAAGAGTAAGAAAAAATGT	0.388																																					p.K97R		Atlas-SNP	.											KIAA0232,bladder,carcinoma,-1,1	KIAA0232	102	1	0			c.A290G						scavenged	.						121.0	124.0	123.0					4																	6843852		1827	4084	5911	SO:0001583	missense	9778	exon4			AGAGTAAGAAAAA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.290A>G	4.37:g.6843852A>G	ENSP00000303928:p.Lys97Arg	37.0	0.0	0		34.0	3.0	0.0882353	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	37	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.957945	0.73902	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	4.9	4.9	0.64082	.	0.166625	0.52532	D	0.000068	T	0.68815	0.3042	L	0.42245	1.32	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.71344	-0.4621	9	0.59425	D	0.04	-25.162	14.5021	0.67729	1.0:0.0:0.0:0.0	.	97	Q92628	K0232_HUMAN	R	97	.	ENSP00000303928:K97R	K	+	2	0	KIAA0232	6894753	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.522000	0.60539	1.817000	0.53016	0.533000	0.62120	AAG	.	.	none		0.388	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743	
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187629137A>G	ENST00000441802.2	-	2	2054	c.1845T>C	c.(1843-1845)ttT>ttC	p.F615F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	615	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGTTTAAACTAAAGAAATCCA	0.433										HNSCC(5;0.00058)			A|||	78	0.0155751	0.0	0.0101	5008	,	,		20191	0.0258		0.0368	False		,,,				2504	0.0082				p.F615F	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1845C						PASS	.	A		23,3713		0,23,1845	68.0	63.0	64.0		1845	-1.3	0.6	4	dbSNP_111	64	305,7891		4,297,3797	no	coding-synonymous	FAT1	NM_005245.3		4,320,5642	GG,GA,AA		3.7213,0.6156,2.7489		615/4589	187629137	328,11604	1868	4098	5966	SO:0001819	synonymous_variant	2195	exon2			TAAACTAAAGAAA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1845T>C	4.37:g.187629137A>G		54.0	0.0	0		41.0	17.0	0.414634	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CD180	4064	hgsc.bcm.edu	37	5	66492387	66492387	+	Missense_Mutation	SNP	C	C	T	rs377501004		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:66492387C>T	ENST00000256447.4	-	1	240	c.83G>A	c.(82-84)tGc>tAc	p.C28Y		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	28					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		CACCTCAATGCACATCTGATC	0.458																																					p.C28Y		Atlas-SNP	.											.	CD180	78	.	0			c.G83A						PASS	.	C	TYR/CYS	2,4404	4.2+/-10.8	0,2,2201	168.0	167.0	167.0		83	5.0	1.0	5		167	0,8600		0,0,4300	no	missense	CD180	NM_005582.2	194	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	28/662	66492387	2,13004	2203	4300	6503	SO:0001583	missense	4064	exon1			TCAATGCACATCT	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.83G>A	5.37:g.66492387C>T	ENSP00000256447:p.Cys28Tyr	64.0	0.0	0		88.0	6.0	0.0681818	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.094491	0.56075	4.54E-4	0.0	ENSG00000134061	ENST00000256447	T	0.60040	0.22	4.99	4.99	0.66335	.	0.148429	0.47455	D	0.000228	T	0.78742	0.4331	M	0.85462	2.755	0.49213	D	0.999768	D	0.89917	1.0	D	0.85130	0.997	T	0.82020	-0.0664	10	0.87932	D	0	.	16.5748	0.84633	0.0:1.0:0.0:0.0	.	28	Q99467	CD180_HUMAN	Y	28	ENSP00000256447:C28Y	ENSP00000256447:C28Y	C	-	2	0	CD180	66528143	1.000000	0.71417	0.991000	0.47740	0.479000	0.33129	3.847000	0.55895	2.754000	0.94517	0.591000	0.81541	TGC	.	.	weak		0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
CFHR2	3080	hgsc.bcm.edu	37	1	196918724	196918724	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196918724T>A	ENST00000367415.5	+	2	298	c.198T>A	c.(196-198)ttT>ttA	p.F66L	CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000476712.2_Missense_Mutation_p.F66L|CFHR2_ENST00000367421.3_Missense_Mutation_p.F66L	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	66	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CAAAATCCTTTTGGACTCGCA	0.378																																					p.F66L		Atlas-SNP	.											.	CFHR2	73	.	0			c.T198A						PASS	.						89.0	83.0	85.0					1																	196918724		2203	4300	6503	SO:0001583	missense	3080	exon2			ATCCTTTTGGACT	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.198T>A	1.37:g.196918724T>A	ENSP00000356385:p.Phe66Leu	235.0	0.0	0		219.0	14.0	0.0639269	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	.	.	.	.	.	.	.	.	.	.	T	2.806	-0.247958	0.05867	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	T;T	0.40756	1.02;1.02	2.77	-0.909	0.10514	Complement control module (2);Sushi/SCR/CCP (2);	1.185540	0.06609	N	0.755236	T	0.27027	0.0662	L	0.33485	1.01	0.09310	N	1	B	0.12013	0.005	B	0.15484	0.013	T	0.24261	-1.0165	10	0.11485	T	0.65	.	5.6889	0.17819	0.0:0.4428:0.0:0.5572	.	66	P36980	FHR2_HUMAN	L	66	ENSP00000356391:F66L;ENSP00000356385:F66L	ENSP00000356385:F66L	F	+	3	2	CFHR2	195185347	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-2.610000	0.00885	-0.221000	0.09973	-0.478000	0.04885	TTT	.	.	none		0.378	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167033	140167033	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140167033T>G	ENST00000504120.2	+	1	1158	c.1158T>G	c.(1156-1158)acT>acG	p.T386T	PCDHA1_ENST00000394633.3_Silent_p.T386T|PCDHA1_ENST00000378133.3_Silent_p.T386T	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	386	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAGGTGACTTGCTCCTTAA	0.567																																					p.T386T		Atlas-SNP	.											.	PCDHA1	387	.	0			c.T1158G						PASS	.						125.0	109.0	114.0					5																	140167033		2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			GGTGACTTGCTCC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1158T>G	5.37:g.140167033T>G		116.0	0.0	0		100.0	18.0	0.18	NM_031411	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																			.	.	none		0.567	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
ATP13A4	84239	hgsc.bcm.edu	37	3	193272556	193272556	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193272556C>T	ENST00000342695.4	-	1	355	c.33G>A	c.(31-33)ctG>ctA	p.L11L	ATP13A4-AS1_ENST00000426459.1_RNA|ATP13A4_ENST00000295548.3_Silent_p.L11L|ATP13A4-AS1_ENST00000431512.1_RNA|ATP13A4_ENST00000392443.3_Silent_p.L11L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	11						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CTTCATTGAGCAGAGCGTGCT	0.507																																					p.L11L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.G33A						PASS	.						304.0	267.0	280.0					3																	193272556		2203	4300	6503	SO:0001819	synonymous_variant	84239	exon1			ATTGAGCAGAGCG	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.33G>A	3.37:g.193272556C>T		124.0	0.0	0		118.0	12.0	0.101695	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			.	.	none		0.507	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
PRAME	23532	hgsc.bcm.edu	37	22	22893394	22893394	+	Missense_Mutation	SNP	A	A	T	rs41310248	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:22893394A>T	ENST00000398741.1	-	4	445	c.139T>A	c.(139-141)Ttg>Atg	p.L47M	PRAME_ENST00000402697.1_Missense_Mutation_p.L47M|PRAME_ENST00000406503.1_Missense_Mutation_p.L47M|PRAME_ENST00000485532.1_5'UTR|PRAME_ENST00000543184.1_Missense_Mutation_p.L47M|PRAME_ENST00000539862.1_Missense_Mutation_p.L31M|PRAME_ENST00000424204.2_Missense_Mutation_p.L31M|PRAME_ENST00000405655.3_Missense_Mutation_p.L47M|PRAME_ENST00000398743.2_Missense_Mutation_p.L47M	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	47					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTGGGCAGCAACTCCAGGGCG	0.617													A|||	32	0.00638978	0.0023	0.0072	5008	,	,		11531	0.0		0.0209	False		,,,				2504	0.0031				p.L47M	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.T139A						PASS	.	A	MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU	29,4377	36.0+/-67.5	0,29,2174	73.0	74.0	73.0		139,139,139,139,139	-5.9	0.0	22	dbSNP_127	73	296,8304	107.6+/-168.3	7,282,4011	yes	missense,missense,missense,missense,missense	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	15,15,15,15,15	7,311,6185	TT,TA,AA		3.4419,0.6582,2.4988	benign,benign,benign,benign,benign	47/510,47/510,47/510,47/510,47/510	22893394	325,12681	2203	4300	6503	SO:0001583	missense	23532	exon4			GCAGCAACTCCAG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.139T>A	22.37:g.22893394A>T	ENSP00000381726:p.Leu47Met	45.0	0.0	0		41.0	25.0	0.609756	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	26|26	0.011904761904761904|0.011904761904761904	3|3	0.006097560975609756|0.006097560975609756	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	19|19	0.025065963060686015|0.025065963060686015	a|a	13.46|13.46	2.244046|2.244046	0.39697|0.39697	0.006582|0.006582	0.034419|0.034419	ENSG00000185686|ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106;ENST00000420709;ENST00000406503;ENST00000403441|ENST00000438888	T;T;T;T;T;T;T;T;T;T;T|.	0.04758|.	3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56|.	3.36|3.36	-5.92|-5.92	0.02261|0.02261	.|.	1.473330|.	0.03603|.	N|.	0.233652|.	T|T	0.13756|0.13756	0.0333|0.0333	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	N|N	1|1	D|.	0.54601|.	0.967|.	P|.	0.55161|.	0.77|.	T|T	0.32824|0.32824	-0.9892|-0.9892	10|5	0.54805|.	T|.	0.06|.	.|.	5.1917|5.1917	0.15212|0.15212	0.6477:0.151:0.1109:0.0904|0.6477:0.151:0.1109:0.0904	rs41310248|rs41310248	47|.	P78395|.	PRAME_HUMAN|.	M|D	47;47;47;47;31;47;31;47;47;47;47|70	ENSP00000381728:L47M;ENSP00000445675:L47M;ENSP00000381726:L47M;ENSP00000384343:L47M;ENSP00000445097:L31M;ENSP00000385198:L47M;ENSP00000407342:L31M;ENSP00000407320:L47M;ENSP00000412318:L47M;ENSP00000384058:L47M;ENSP00000385091:L47M|.	ENSP00000381726:L47M|.	L|V	-|-	1|2	2|0	PRAME|PRAME	21223394|21223394	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.668000|0.668000	0.39293|0.39293	-2.016000|-2.016000	0.01446|0.01446	-1.139000|-1.139000	0.02881|0.02881	-0.213000|-0.213000	0.12676|0.12676	TTG|GTT	A|0.978;T|0.022	0.022	strong		0.617	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
CLCN7	1186	hgsc.bcm.edu	37	16	1506130	1506130	+	Silent	SNP	C	C	T	rs41286695	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1506130C>T	ENST00000382745.4	-	10	1505	c.900G>A	c.(898-900)gcG>gcA	p.A300A	CLCN7_ENST00000262318.8_Silent_p.A276A|CLCN7_ENST00000448525.1_Silent_p.A276A	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	300					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GGGCTCCAAACGCCGCTGACA	0.642													C|||	79	0.0157748	0.0015	0.0159	5008	,	,		16001	0.0		0.0616	False		,,,				2504	0.0041				p.A300A		Atlas-SNP	.											.	CLCN7	53	.	0			c.G900A						PASS	.	C	,	37,4273		0,37,2118	12.0	14.0	14.0		828,900	-10.2	0.0	16	dbSNP_127	14	420,8048		4,412,3818	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	4,449,5936	TT,TC,CC		4.9598,0.8585,3.5765	,	276/782,300/806	1506130	457,12321	2155	4234	6389	SO:0001819	synonymous_variant	1186	exon10			TCCAAACGCCGCT	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.900G>A	16.37:g.1506130C>T		26.0	0.0	0		24.0	14.0	0.583333	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			C|0.973;T|0.027	0.027	strong		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
B4GALNT4	338707	hgsc.bcm.edu	37	11	380395	380395	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:380395C>T	ENST00000329962.6	+	18	2819	c.2819C>T	c.(2818-2820)gCg>gTg	p.A940V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	940					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGGCCTTCGCGCCCGTGGTC	0.687																																					p.A940V		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	0			c.C2819T						PASS	.						55.0	40.0	45.0					11																	380395		2202	4299	6501	SO:0001583	missense	338707	exon18			CCTTCGCGCCCGT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2819C>T	11.37:g.380395C>T	ENSP00000328277:p.Ala940Val	70.0	0.0	0		55.0	4.0	0.0727273	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	25.9	4.682412	0.88542	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.67517	2.055	0.58432	D	0.99999	P	0.46512	0.879	P	0.45856	0.495	T	0.36432	-0.9748	10	0.20519	T	0.43	-32.7173	16.2551	0.82510	0.0:1.0:0.0:0.0	.	940	Q76KP1	B4GN4_HUMAN	V	940	ENSP00000328277:A940V	ENSP00000328277:A940V	A	+	2	0	B4GALNT4	370395	1.000000	0.71417	0.977000	0.42913	0.811000	0.45836	7.456000	0.80751	2.118000	0.64928	0.561000	0.74099	GCG	.	.	none		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
NT5M	56953	hgsc.bcm.edu	37	17	17250197	17250197	+	Missense_Mutation	SNP	G	G	A	rs145194793	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17250197G>A	ENST00000389022.4	+	5	839	c.623G>A	c.(622-624)cGc>cAc	p.R208H	NT5M_ENST00000582909.1_3'UTR	NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	208					dephosphorylation (GO:0016311)|DNA replication (GO:0006260)|dUMP catabolic process (GO:0046079)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|nucleotide binding (GO:0000166)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CAGCCCCCCCGCCGCAGGCTG	0.677													G|||	8	0.00159744	0.0	0.0	5008	,	,		15949	0.0		0.007	False		,,,				2504	0.001				p.R208H		Atlas-SNP	.											.	NT5M	17	.	0			c.G623A						PASS	.	G	HIS/ARG	7,4395		0,7,2194	30.0	36.0	34.0		623	-0.1	0.4	17	dbSNP_134	34	40,8552		0,40,4256	yes	missense	NT5M	NM_020201.3	29	0,47,6450	AA,AG,GG		0.4655,0.159,0.3617	possibly-damaging	208/229	17250197	47,12947	2201	4296	6497	SO:0001583	missense	56953	exon5			CCCCCCGCCGCAG	AF210652	CCDS32581.1	17p11.2	2007-08-01	2002-05-23		ENSG00000205309	ENSG00000205309	3.1.3.5		15769	protein-coding gene	gene with protein product		605292	"""5' nucleotidase, mitochondrial"""			10899995	Standard	XM_005256731		Approved	dNT-2, dNT2, mdN	uc002grf.3	Q9NPB1	OTTHUMG00000059277	ENST00000389022.4:c.623G>A	17.37:g.17250197G>A	ENSP00000373674:p.Arg208His	63.0	0.0	0		77.0	40.0	0.519481	NM_020201		Missense_Mutation	SNP	ENST00000389022.4	37	CCDS32581.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	G|G	13.76|13.76	2.332091|2.332091	0.41297|0.41297	0.00159|0.00159	0.004655|0.004655	ENSG00000205309|ENSG00000205309	ENST00000446264|ENST00000389022	.|T	.|0.41400	.|1.0	5.79|5.79	-0.0825|-0.0825	0.13697|0.13697	.|HAD-like domain (2);	0.532662|.	0.21888|.	N|.	0.067623|.	T|T	0.25901|0.25901	0.0631|0.0631	L|L	0.31420|0.31420	0.93|0.93	0.09310|0.09310	N|N	1|1	B|D;P	0.27971|0.52996	0.196|0.957;0.926	B|P;P	0.17098|0.48270	0.017|0.572;0.572	T|T	0.15235|0.15235	-1.0444|-1.0444	9|9	0.59425|0.59425	D|D	0.04|0.04	-10.4946|-10.4946	6.402|6.402	0.21644|0.21644	0.3077:0.0:0.5678:0.1245|0.3077:0.0:0.5678:0.1245	.|.	207|214;208	F6S3X3|Q2I378;Q9NPB1	.|.;NT5M_HUMAN	T|H	207|208	.|ENSP00000373674:R208H	ENSP00000390695:A207T|ENSP00000373674:R208H	A|R	+|+	1|2	0|0	NT5M|NT5M	17190922|17190922	0.735000|0.735000	0.28153|0.28153	0.378000|0.378000	0.26068|0.26068	0.070000|0.070000	0.16714|0.16714	1.114000|1.114000	0.31196|0.31196	0.377000|0.377000	0.24735|0.24735	-0.254000|-0.254000	0.11334|0.11334	GCC|CGC	G|0.997;A|0.003	0.003	strong		0.677	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1		
PTBP2	58155	hgsc.bcm.edu	37	1	97235290	97235290	+	Silent	SNP	A	A	G	rs139414147	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:97235290A>G	ENST00000426398.2	+	4	190	c.147A>G	c.(145-147)ggA>ggG	p.G49G	PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370197.1_Silent_p.G49G|PTBP2_ENST00000370198.1_Silent_p.G49G|PTBP2_ENST00000541987.1_Silent_p.G18G|PTBP2_ENST00000394184.3_Silent_p.G60G|PTBP2_ENST00000609116.1_Silent_p.G49G	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	49					mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		AATTTAAAGGAGAAGATAAAA	0.313													A|||	8	0.00159744	0.0	0.0014	5008	,	,		15902	0.0		0.0	False		,,,				2504	0.0072				p.G49G		Atlas-SNP	.											.	PTBP2	62	.	0			c.A147G						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	87.0	96.0	93.0		147	3.0	1.0	1	dbSNP_134	93	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	PTBP2	NM_021190.2		0,26,6477	GG,GA,AA		0.2907,0.0227,0.1999		49/532	97235290	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	58155	exon4			TAAAGGAGAAGAT	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"""RNA binding motif (RRM) containing"""	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.147A>G	1.37:g.97235290A>G		100.0	0.0	0		89.0	33.0	0.370787	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Silent	SNP	ENST00000426398.2	37	CCDS754.1																																																																																			A|0.998;G|0.002	0.002	strong		0.313	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		
LIMD2	80774	hgsc.bcm.edu	37	17	61776651	61776651	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:61776651T>A	ENST00000259006.3	-	2	166	c.8A>T	c.(7-9)cAg>cTg	p.Q3L	LIMD2_ENST00000582055.1_5'Flank|LIMD2_ENST00000578061.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000578402.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000578993.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000583211.1_5'UTR	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	3							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						TCCTGCAGCCTGGAACATGGC	0.716																																					p.Q3L		Atlas-SNP	.											.	LIMD2	6	.	0			c.A8T						PASS	.						12.0	16.0	15.0					17																	61776651		2182	4271	6453	SO:0001583	missense	80774	exon2			GCAGCCTGGAACA	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.8A>T	17.37:g.61776651T>A	ENSP00000259006:p.Gln3Leu	112.0	0.0	0		96.0	20.0	0.208333	NM_030576	D3DU16|Q96S91	Missense_Mutation	SNP	ENST00000259006.3	37	CCDS11641.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298889	0.60195	.	.	ENSG00000136490	ENST00000259006	T	0.77358	-1.09	4.43	4.43	0.53597	.	0.000000	0.64402	D	0.000011	T	0.66218	0.2767	L	0.27053	0.805	0.80722	D	1	B	0.18461	0.028	B	0.11329	0.006	T	0.66176	-0.5989	10	0.87932	D	0	-18.1445	12.0851	0.53691	0.0:0.0:0.0:1.0	.	3	Q9BT23	LIMD2_HUMAN	L	3	ENSP00000259006:Q3L	ENSP00000259006:Q3L	Q	-	2	0	LIMD2	59130383	0.970000	0.33590	1.000000	0.80357	0.975000	0.68041	1.307000	0.33516	1.856000	0.53863	0.379000	0.24179	CAG	.	.	none		0.716	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576	
OMA1	115209	hgsc.bcm.edu	37	1	58999896	58999896	+	Silent	SNP	C	C	A	rs41287650		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:58999896C>A	ENST00000371226.3	-	4	950	c.837G>T	c.(835-837)ggG>ggT	p.G279G	DAB1_ENST00000485760.1_Intron|OMA1_ENST00000358603.2_Silent_p.G279G|OMA1_ENST00000467063.1_5'UTR	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	279					cristae formation (GO:0042407)|diet induced thermogenesis (GO:0002024)|energy homeostasis (GO:0097009)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrial protein processing (GO:0034982)|negative regulation of mitochondrial fusion (GO:0010637)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(1)|large_intestine(6)|liver(2)|lung(6)|prostate(1)|skin(1)	18	all_cancers(7;6.54e-05)					TCTGAGAGATCCCTGGAACAT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		16906	0.0		0.001	False		,,,				2504	0.0				p.G279G		Atlas-SNP	.											.	OMA1	50	.	0			c.G837T						PASS	.	C		0,4406		0,0,2203	78.0	77.0	77.0		837	-1.8	0.1	1	dbSNP_127	77	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	OMA1	NM_145243.3		0,7,6496	AA,AC,CC		0.0814,0.0,0.0538		279/525	58999896	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	115209	exon4			AGAGATCCCTGGA	AK091101	CCDS608.1	1p32.2-p32.1	2013-05-03	2013-05-03		ENSG00000162600	ENSG00000162600			29661	protein-coding gene	gene with protein product	"""overlapping activity with M-AAA protease"", ""zinc metallopeptidase OMA1"""		"""OMA1 zinc metallopeptidase homolog (S. cerevisiae)"""			12477932	Standard	NM_145243		Approved	MPRP-1, YKR087C, ZMPOMA1, FLJ33782	uc001cyy.3	Q96E52	OTTHUMG00000010068	ENST00000371226.3:c.837G>T	1.37:g.58999896C>A		281.0	0.0	0		231.0	89.0	0.385281	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Silent	SNP	ENST00000371226.3	37	CCDS608.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	5.604	0.296110	0.10622	0.0	8.14E-4	ENSG00000162600	ENST00000421528	.	.	.	4.9	-1.81	0.07882	.	.	.	.	.	T	0.28928	0.0718	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-8.8864	6.6045	0.22718	0.0:0.3943:0.2766:0.329	rs41287650	.	.	.	Y	121	.	.	D	-	1	0	OMA1	58772484	0.193000	0.23313	0.076000	0.20297	0.911000	0.54048	0.160000	0.16462	-0.139000	0.11414	0.563000	0.77884	GAT	C|1.000;A|0.000	0.000	strong		0.358	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243	
RSAD1	55316	hgsc.bcm.edu	37	17	48561871	48561871	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48561871G>A	ENST00000258955.2	+	8	1261	c.1176G>A	c.(1174-1176)gaG>gaA	p.E392E		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	392					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AGGTGCAGGAGCTGCTGGAGC	0.647																																					p.E392E		Atlas-SNP	.											RSAD1,NS,carcinoma,+2,1	RSAD1	36	1	0			c.G1176A						PASS	.						56.0	58.0	58.0					17																	48561871		2203	4300	6503	SO:0001819	synonymous_variant	55316	exon8			GCAGGAGCTGCTG	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.1176G>A	17.37:g.48561871G>A		34.0	0.0	0		43.0	12.0	0.27907	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Silent	SNP	ENST00000258955.2	37	CCDS11569.1																																																																																			.	.	none		0.647	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
OTUD4	54726	hgsc.bcm.edu	37	4	146063471	146063471	+	Missense_Mutation	SNP	C	C	T	rs151020153	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:146063471C>T	ENST00000447906.2	-	18	1886	c.1699G>A	c.(1699-1701)Gtg>Atg	p.V567M	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Missense_Mutation_p.V502M			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	567					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					GACAAAGACACATGTTCTGCT	0.468													C|||	4	0.000798722	0.0	0.0	5008	,	,		19395	0.0		0.004	False		,,,				2504	0.0				p.V502M		Atlas-SNP	.											.	OTUD4	120	.	0			c.G1504A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	111.0	120.0	117.0		1504	5.3	1.0	4	dbSNP_134	117	35,8565	24.0+/-70.4	0,35,4265	yes	missense	OTUD4	NM_001102653.1	21	0,36,6467	TT,TC,CC		0.407,0.0227,0.2768	possibly-damaging	502/1050	146063471	36,12970	2203	4300	6503	SO:0001583	missense	54726	exon18			AAGACACATGTTC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.1699G>A	4.37:g.146063471C>T	ENSP00000395487:p.Val567Met	50.0	0.0	0		65.0	35.0	0.538462	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	18.08	3.544424	0.65198	2.27E-4	0.00407	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34072	1.39;1.38	6.16	5.31	0.75309	.	0.224719	0.32055	N	0.006652	T	0.24928	0.0605	N	0.24115	0.695	0.80722	D	1	P;P	0.42203	0.773;0.664	P;B	0.48840	0.592;0.388	T	0.10683	-1.0619	10	0.62326	D	0.03	-7.2241	7.8627	0.29520	0.2599:0.6608:0.0:0.0793	.	567;566	G3V0I6;Q01804	.;OTUD4_HUMAN	M	502;567	ENSP00000409279:V502M;ENSP00000395487:V567M	ENSP00000395487:V567M	V	-	1	0	OTUD4	146282921	0.877000	0.30153	1.000000	0.80357	0.974000	0.67602	0.769000	0.26604	1.594000	0.50039	0.650000	0.86243	GTG	C|0.998;T|0.002	0.002	strong		0.468	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493	
BICD1	636	hgsc.bcm.edu	37	12	32481369	32481369	+	Silent	SNP	C	C	T	rs34447944	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:32481369C>T	ENST00000281474.5	+	5	2083	c.1980C>T	c.(1978-1980)gcC>gcT	p.A660A	BICD1_ENST00000548411.1_Silent_p.A660A	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	660					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GGGAGCTAGCCCCCATGATTG	0.527													C|||	232	0.0463259	0.0023	0.0389	5008	,	,		15395	0.0079		0.0865	False		,,,				2504	0.1094				p.A660A		Atlas-SNP	.											BICD1,colon,carcinoma,0,1	BICD1	89	1	0			c.C1980T						PASS	.	C	,	67,4339	62.9+/-100.1	0,67,2136	66.0	70.0	69.0		1980,1980	0.8	1.0	12	dbSNP_126	69	743,7857	176.2+/-226.1	30,683,3587	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	30,750,5723	TT,TC,CC		8.6395,1.5207,6.2279	,	660/836,660/976	32481369	810,12196	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			GCTAGCCCCCATG	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1980C>T	12.37:g.32481369C>T		110.0	0.0	0		93.0	32.0	0.344086	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			C|0.940;T|0.060	0.060	strong		0.527	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
MLXIPL	51085	hgsc.bcm.edu	37	7	73010191	73010191	+	Missense_Mutation	SNP	C	C	T	rs149244334	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73010191C>T	ENST00000313375.3	-	14	2214	c.2167G>A	c.(2167-2169)Gag>Aag	p.E723K	MLXIPL_ENST00000414749.2_Missense_Mutation_p.E721K|MLXIPL_ENST00000434326.1_Missense_Mutation_p.E629K|MLXIPL_ENST00000354613.1_Missense_Mutation_p.E702K|MLXIPL_ENST00000429400.2_Missense_Mutation_p.E704K|MLXIPL_ENST00000395189.1_Missense_Mutation_p.E630K	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	723	Leucine-zipper.				anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCATTGAGCTCCTCAATCTCA	0.647													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		14413	0.0		0.002	False		,,,				2504	0.0				p.E723K		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G2167A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4403		0,1,2201	34.0	30.0	31.0		2167,2110,2161,2104	5.0	1.0	7	dbSNP_134	31	9,8591		0,9,4291	yes	missense,missense,missense,missense	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	56,56,56,56	0,10,6492	TT,TC,CC		0.1047,0.0227,0.0769	probably-damaging,probably-damaging,probably-damaging,probably-damaging	723/853,704/834,721/851,702/832	73010191	10,12994	2202	4300	6502	SO:0001583	missense	51085	exon14			TGAGCTCCTCAAT	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.2167G>A	7.37:g.73010191C>T	ENSP00000320886:p.Glu723Lys	52.0	0.0	0		35.0	16.0	0.457143	NM_032951	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	37	CCDS5553.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	21.5	4.162639	0.78226	2.27E-4	0.001047	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326	D;D;D;D;D;D	0.98493	-4.95;-4.96;-4.95;-4.96;-4.95;-4.95	5.04	5.04	0.67666	.	0.372017	0.26362	N	0.024805	D	0.98283	0.9431	M	0.78916	2.43	0.37356	D	0.911005	D;D;D;D;D	0.63880	0.993;0.979;0.99;0.971;0.971	D;P;D;P;P	0.72982	0.922;0.549;0.979;0.754;0.832	D	0.97181	0.9851	10	0.72032	D	0.01	-16.78	15.9196	0.79552	0.0:1.0:0.0:0.0	.	630;723;704;721;702	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	K	721;704;723;702;630;629	ENSP00000412330:E721K;ENSP00000406296:E704K;ENSP00000320886:E723K;ENSP00000346629:E702K;ENSP00000378616:E630K;ENSP00000392636:E629K	ENSP00000320886:E723K	E	-	1	0	MLXIPL	72648127	0.981000	0.34729	1.000000	0.80357	0.993000	0.82548	2.179000	0.42528	2.350000	0.79820	0.558000	0.71614	GAG	C|0.999;T|0.001	0.001	strong		0.647	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
CTAGE5	4253	hgsc.bcm.edu	37	14	39769122	39769122	+	Missense_Mutation	SNP	A	A	C	rs34761053	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39769122A>C	ENST00000280083.3	+	9	1041	c.727A>C	c.(727-729)Aaa>Caa	p.K243Q	CTAGE5_ENST00000396158.2_Missense_Mutation_p.K248Q|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K778Q|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K243Q|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K231Q|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K214Q|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000557038.1_Missense_Mutation_p.K163Q|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K168Q|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000348007.3_Missense_Mutation_p.K243Q			O15320	CTGE5_HUMAN	CTAGE family, member 5	243					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TAATAAACAGAAAGTAACATT	0.328													A|||	7	0.00139776	0.0	0.0	5008	,	,		16808	0.0		0.007	False		,,,				2504	0.0				p.K248Q		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A742C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	2,4404	4.2+/-10.8	0,2,2201	132.0	136.0	135.0		727,691,727,640	5.5	1.0	14	dbSNP_126	135	60,8534	36.4+/-91.3	0,60,4237	no	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	53,53,53,53	0,62,6438	CC,CA,AA		0.6982,0.0454,0.4769	benign,benign,benign,benign	243/805,231/793,243/762,214/776	39769122	62,12938	2203	4297	6500	SO:0001583	missense	4253	exon9			AAACAGAAAGTAA	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.727A>C	14.37:g.39769122A>C	ENSP00000280083:p.Lys243Gln	85.0	0.0	0		60.0	25.0	0.416667	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	18.38	3.611043	0.66558	4.54E-4	0.006982	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.77877	1.18;-1.13;1.18;-1.13;-1.13;1.18;-1.13;1.18;-1.13;-1.13	5.49	5.49	0.81192	.	0.241343	0.21531	N	0.073042	T	0.77212	0.4097	M	0.84219	2.685	0.31455	N	0.67022	B;B;B;B;B;B	0.33826	0.427;0.191;0.184;0.112;0.384;0.112	B;B;B;B;B;B	0.40506	0.331;0.183;0.251;0.183;0.251;0.183	T	0.82474	-0.0439	9	.	.	.	.	13.8371	0.63415	1.0:0.0:0.0:0.0	rs34761053	205;248;243;243;214;231	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	Q	778;231;163;205;214;243;248;243;168;243;214	ENSP00000452252:K778Q;ENSP00000343897:K231Q;ENSP00000450869:K163Q;ENSP00000379468:K214Q;ENSP00000339286:K243Q;ENSP00000379462:K248Q;ENSP00000280083:K243Q;ENSP00000452562:K168Q;ENSP00000343912:K243Q;ENSP00000450449:K214Q	.	K	+	1	0	CTAGE5;RP11-407N17.3	38838873	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	5.768000	0.68858	2.075000	0.62263	0.528000	0.53228	AAA	A|0.995;C|0.005	0.005	strong		0.328	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
CELSR1	9620	hgsc.bcm.edu	37	22	46762360	46762360	+	Silent	SNP	G	G	A	rs56325154	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46762360G>A	ENST00000262738.3	-	30	8222	c.8223C>T	c.(8221-8223)aaC>aaT	p.N2741N		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2741					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGAAGGTGGTGTTGCAGTTGA	0.652													.|||	56	0.0111821	0.0008	0.0058	5008	,	,		12394	0.002		0.0139	False		,,,				2504	0.0358				p.N2741N		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8223T						PASS	.			10,4078		0,10,2034	52.0	38.0	43.0		8223	4.5	1.0	22	dbSNP_129	43	87,7807		0,87,3860	no	coding-synonymous	CELSR1	NM_014246.1		0,97,5894	AA,AG,GG		1.1021,0.2446,0.8095		2741/3015	46762360	97,11885	2044	3947	5991	SO:0001819	synonymous_variant	9620	exon30			GGTGGTGTTGCAG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8223C>T	22.37:g.46762360G>A		95.0	0.0	0		107.0	52.0	0.485981	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.993;A|0.007	0.007	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783628	140783628	+	Missense_Mutation	SNP	A	A	G	rs375910829		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140783628A>G	ENST00000573521.1	+	1	1109	c.1109A>G	c.(1108-1110)aAt>aGt	p.N370S	PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCTTTTCAATGCTCATGAC	0.398													.|||	1	0.000199681	0.0008	0.0	5008	,	,		19094	0.0		0.0	False		,,,				2504	0.0				p.N370S		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.A1109G						PASS	.	A	,,,,,,,,SER/ASN,,,,,,SER/ASN	1,3923		0,1,1961	51.0	52.0	52.0		,,,,,,,,1109,,,,,,1109	5.3	1.0	5		52	0,8306		0,0,4153	no	intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,46,,,,,,46	0,1,6114	GG,GA,AA		0.0,0.0255,0.0082	,,,,,,,,,,,,,,	,,,,,,,,370/933,,,,,,370/829	140783628	1,12229	1962	4153	6115	SO:0001583	missense	56107	exon1			TTTTCAATGCTCA	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1109A>G	5.37:g.140783628A>G	ENSP00000460274:p.Asn370Ser	124.0	0.0	0		139.0	71.0	0.510791	NM_032089	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			.	.	weak		0.398	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
ENPP5	59084	hgsc.bcm.edu	37	6	46135795	46135795	+	Missense_Mutation	SNP	T	T	C	rs34432940	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:46135795T>C	ENST00000371383.2	-	3	465	c.205A>G	c.(205-207)Att>Gtt	p.I69V	ENPP5_ENST00000230565.3_Missense_Mutation_p.I69V|ENPP5_ENST00000492313.1_5'Flank					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GTTTTTGTAATAAAAACATTA	0.348													T|||	10	0.00199681	0.0	0.0043	5008	,	,		19208	0.0		0.007	False		,,,				2504	0.0				p.I69V		Atlas-SNP	.											.	ENPP5	44	.	0			c.A205G						PASS	.	T	VAL/ILE	11,4395	17.9+/-39.9	0,11,2192	53.0	50.0	51.0		205	3.1	1.0	6	dbSNP_126	51	76,8524	44.0+/-102.2	0,76,4224	yes	missense	ENPP5	NM_021572.4	29	0,87,6416	CC,CT,TT		0.8837,0.2497,0.6689	benign	69/478	46135795	87,12919	2203	4300	6503	SO:0001583	missense	59084	exon2			TTGTAATAAAAAC	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.205A>G	6.37:g.46135795T>C	ENSP00000360436:p.Ile69Val	60.0	0.0	0		81.0	40.0	0.493827	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	11.84	1.757670	0.31137	0.002497	0.008837	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.72167	-0.63;-0.63	5.51	3.07	0.35406	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.050250	0.85682	D	0.000000	T	0.32882	0.0844	N	0.20685	0.6	0.36437	D	0.865251	B;B	0.19331	0.035;0.035	B;B	0.24006	0.05;0.05	T	0.08743	-1.0707	10	0.21014	T	0.42	-24.9657	8.0281	0.30448	0.0:0.1187:0.1209:0.7604	rs34432940	69;69	A8K9X7;Q9UJA9	.;ENPP5_HUMAN	V	69	ENSP00000360436:I69V;ENSP00000230565:I69V	ENSP00000230565:I69V	I	-	1	0	ENPP5	46243754	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.504000	0.45416	1.010000	0.39314	0.482000	0.46254	ATT	T|0.993;C|0.007	0.007	strong		0.348	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
PSME4	23198	hgsc.bcm.edu	37	2	54176359	54176359	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54176359A>G	ENST00000404125.1	-	2	359	c.304T>C	c.(304-306)Ttg>Ctg	p.L102L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	102					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGCTCATACAATAACTTAATA	0.328																																					p.L102L		Atlas-SNP	.											.	PSME4	247	.	0			c.T304C						PASS	.						67.0	68.0	67.0					2																	54176359		2203	4300	6503	SO:0001819	synonymous_variant	23198	exon2			CATACAATAACTT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.304T>C	2.37:g.54176359A>G		59.0	0.0	0		74.0	23.0	0.310811	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			.	.	none		0.328	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325285	77325285	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:77325285G>A	ENST00000282849.5	-	21	3698	c.3280C>T	c.(3280-3282)Cga>Tga	p.R1094*	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1094	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CGGCATCTTCGCTCTGGGAAA	0.517																																					p.R1094X		Atlas-SNP	.											ADAMTS18,NS,carcinoma,+1,2	ADAMTS18	270	2	0			c.C3280T						PASS	.						218.0	222.0	221.0					16																	77325285		2198	4300	6498	SO:0001587	stop_gained	170692	exon21			ATCTTCGCTCTGG	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3280C>T	16.37:g.77325285G>A	ENSP00000282849:p.Arg1094*	138.0	0.0	0		129.0	31.0	0.24031	NM_199355	Q6P4R5|Q6ZWJ9	Nonsense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	44	10.621894	0.99439	.	.	ENSG00000140873	ENST00000282849	.	.	.	5.8	4.83	0.62350	.	0.061993	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5838	0.56406	0.0:0.0:0.5802:0.4198	.	.	.	.	X	1094	.	ENSP00000282849:R1094X	R	-	1	2	ADAMTS18	75882786	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	3.887000	0.56197	1.427000	0.47276	0.563000	0.77884	CGA	.	.	none		0.517	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
SETD5	55209	hgsc.bcm.edu	37	3	9483818	9483818	+	Nonsense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9483818C>G	ENST00000406341.1	+	9	1156	c.966C>G	c.(964-966)taC>taG	p.Y322*	SETD5_ENST00000407969.1_Nonsense_Mutation_p.Y341*|SETD5_ENST00000402198.1_Nonsense_Mutation_p.Y322*|SETD5_ENST00000402466.1_Nonsense_Mutation_p.Y224*|SETD5_ENST00000302463.6_Nonsense_Mutation_p.Y224*			Q9C0A6	SETD5_HUMAN	SET domain containing 5	322	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.									NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CTAGACCATACCCCTTTGTGC	0.418																																					p.Y322X		Atlas-SNP	.											.	SETD5	210	.	0			c.C966G						PASS	.						131.0	115.0	120.0					3																	9483818		1900	4124	6024	SO:0001587	stop_gained	55209	exon10			ACCATACCCCTTT	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.966C>G	3.37:g.9483818C>G	ENSP00000383939:p.Tyr322*	31.0	0.0	0		47.0	17.0	0.361702	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Nonsense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	C	43	10.335419	0.99385	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	.	.	.	5.49	1.36	0.22044	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8775	8.1691	0.31243	0.0:0.3117:0.0:0.6883	.	.	.	.	X	322;224;322;341;224	.	ENSP00000302028:Y224X	Y	+	3	2	SETD5	9458818	0.972000	0.33761	1.000000	0.80357	0.992000	0.81027	0.196000	0.17176	0.188000	0.20168	-0.137000	0.14449	TAC	.	.	none		0.418	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:24954303G>C	ENST00000217456.2	-	4	689	c.399C>G	c.(397-399)gcC>gcG	p.A133A	APMAP_ENST00000447138.1_Silent_p.A133A|RNU6-1257P_ENST00000384625.1_RNA	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	133					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										AACCAAACCGGGCAATGGTCT	0.448													G|||	3	0.000599042	0.0	0.0	5008	,	,		19675	0.0		0.001	False		,,,				2504	0.002				p.A133A		Atlas-SNP	.											.	APMAP	3	.	0			c.C399G						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	107.0	92.0	97.0		399	0.0	1.0	20	dbSNP_134	97	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	C20orf3	NM_020531.2		0,13,6490	CC,CG,GG		0.1279,0.0454,0.1		133/417	24954303	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			AAACCGGGCAATG	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.399C>G	20.37:g.24954303G>C		98.0	0.0	0		102.0	57.0	0.558824	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103322	0.20632	4.54E-4	0.001279	ENSG00000101474	ENST00000451442	.	.	.	5.43	0.0444	0.14225	.	.	.	.	.	T	0.50360	0.1611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33752	-0.9856	4	.	.	.	-17.6727	5.067	0.14587	0.3047:0.2599:0.4354:0.0	.	.	.	.	R	118	.	.	P	-	2	0	C20orf3	24902303	0.804000	0.28969	0.963000	0.40424	0.854000	0.48673	-0.233000	0.09041	-0.200000	0.10300	-0.150000	0.13652	CCC	G|0.998;C|0.002	0.002	strong		0.448	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
SBF1	6305	hgsc.bcm.edu	37	22	50893668	50893668	+	Silent	SNP	C	C	G	rs374064130		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50893668C>G	ENST00000390679.3	-	32	4645	c.4461G>C	c.(4459-4461)ctG>ctC	p.L1487L	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000380817.3_Silent_p.L1513L|SBF1_ENST00000348911.6_Silent_p.L1488L			O95248	MTMR5_HUMAN	SET binding factor 1	1487	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTACGCAGTCCAGGAACTGCA	0.677																																					p.L1513L		Atlas-SNP	.											.	SBF1	211	.	0			c.G4539C						PASS	.	C		0,4196		0,0,2098	24.0	32.0	29.0		4539	1.8	1.0	22		29	4,8394		0,4,4195	no	coding-synonymous	SBF1	NM_002972.2		0,4,6293	GG,GC,CC		0.0476,0.0,0.0318		1513/1894	50893668	4,12590	2098	4199	6297	SO:0001819	synonymous_variant	6305	exon33			GCAGTCCAGGAAC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.4461G>C	22.37:g.50893668C>G		57.0	0.0	0		56.0	35.0	0.625	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	8.810	0.934901	0.18206	0.0	4.76E-4	ENSG00000100241	ENST00000418590	.	.	.	3.84	1.75	0.24633	.	.	.	.	.	T	0.56411	0.1983	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52087	-0.8622	4	.	.	.	.	8.9063	0.35526	0.0:0.7398:0.0:0.2602	.	.	.	.	R	47	.	.	G	-	1	0	SBF1	49240534	0.349000	0.24870	1.000000	0.80357	0.978000	0.69477	-0.281000	0.08456	0.969000	0.38237	0.563000	0.77884	GGA	.	.	weak		0.677	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCCTCTTCCGGTGCCCGCCG	0.647		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	PASS	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0.0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	60.0	0.0	0		46.0	25.0	0.543478	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
WNK2	65268	hgsc.bcm.edu	37	9	96030979	96030979	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96030979A>T	ENST00000297954.4	+	18	3984	c.3984A>T	c.(3982-3984)gaA>gaT	p.E1328D	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.E940D|WNK2_ENST00000349097.3_Missense_Mutation_p.E940D|WNK2_ENST00000395477.2_Missense_Mutation_p.E1328D|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1328					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						AGGCCCCTGAATCTTCGCCCC	0.622																																					p.E1328D		Atlas-SNP	.											.	WNK2	277	.	0			c.A3984T						PASS	.						36.0	34.0	34.0					9																	96030979		2203	4300	6503	SO:0001583	missense	65268	exon18			CCCTGAATCTTCG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3984A>T	9.37:g.96030979A>T	ENSP00000297954:p.Glu1328Asp	109.0	0.0	0		91.0	28.0	0.307692	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	17.42|17.42|17.42	3.384909|3.384909|3.384909	0.61956|0.61956|0.61956	.|.|.	.|.|.	ENSG00000165238|ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000411624|ENST00000432730;ENST00000448251	T;T;T;T|.|.	0.41400|.|.	1.0;1.0;1.0;1.0|.|.	5.95|5.95|5.95	-9.28|-9.28|-9.28	0.00656|0.00656|0.00656	.|.|.	0.600559|.|.	0.17654|.|.	N|.|.	0.166571|.|.	T|T|T	0.60287|0.60287|0.60287	0.2257|0.2257|0.2257	L|L|L	0.51422|0.51422|0.51422	1.61|1.61|1.61	0.49687|0.49687|0.49687	D|D|D	0.999815|0.999815|0.999815	D;B;B;D|.|.	0.67145|.|.	0.996;0.028;0.047;0.991|.|.	P;B;B;P|.|.	0.60117|.|.	0.869;0.012;0.027;0.675|.|.	T|T|T	0.68872|0.68872|0.68872	-0.5294|-0.5294|-0.5294	10|5|5	0.13470|.|.	T|.|.	0.59|.|.	.|.|.	15.7974|15.7974|15.7974	0.78423|0.78423|0.78423	0.3327:0.0843:0.583:0.0|0.3327:0.0843:0.583:0.0|0.3327:0.0843:0.583:0.0	.|.|.	1328;931;1328;1328|.|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.|.	.;.;.;WNK2_HUMAN|.|.	D|F|I	1328;1328;940;940|932|1324;125	ENSP00000297954:E1328D;ENSP00000378860:E1328D;ENSP00000297876:E940D;ENSP00000411181:E940D|.|.	ENSP00000297954:E1328D|.|.	E|I|N	+|+|+	3|1|2	2|0|0	WNK2|WNK2|WNK2	95070800|95070800|95070800	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.388000|0.388000|0.388000	0.30384|0.30384|0.30384	-1.194000|-1.194000|-1.194000	0.03046|0.03046|0.03046	-1.603000|-1.603000|-1.603000	0.01597|0.01597|0.01597	-0.250000|-0.250000|-0.250000	0.11733|0.11733|0.11733	GAA|ATC|AAT	.	.	none		0.622	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
COL6A6	131873	hgsc.bcm.edu	37	3	130311551	130311551	+	Silent	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:130311551A>T	ENST00000358511.6	+	14	4387	c.4356A>T	c.(4354-4356)ggA>ggT	p.G1452G	COL6A6_ENST00000453409.2_Silent_p.G1452G	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1452	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GAAACAGAGGACTAAATGGAC	0.313																																					p.G1452G		Atlas-SNP	.											COL6A6_ENST00000358511,bladder,carcinoma,+1,2	COL6A6	497	2	0			c.A4356T						PASS	.						162.0	153.0	156.0					3																	130311551		1844	4080	5924	SO:0001819	synonymous_variant	131873	exon14			CAGAGGACTAAAT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4356A>T	3.37:g.130311551A>T		131.0	0.0	0		108.0	28.0	0.259259	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	1.893	-0.455057	0.04540	.	.	ENSG00000206384	ENST00000511332	.	.	.	5.83	3.41	0.39046	.	.	.	.	.	T	0.55178	0.1904	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50180	-0.8858	4	.	.	.	.	6.402	0.21644	0.7606:0.1572:0.0822:0.0	.	.	.	.	V	231	.	.	D	+	2	0	COL6A6	131794241	0.998000	0.40836	0.987000	0.45799	0.114000	0.19823	1.173000	0.31920	1.021000	0.39600	0.460000	0.39030	GAC	.	.	none		0.313	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
OR2L3	391192	hgsc.bcm.edu	37	1	248224227	248224227	+	Missense_Mutation	SNP	T	T	C	rs146249174	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224227T>C	ENST00000359959.3	+	1	244	c.244T>C	c.(244-246)Tct>Cct	p.S82P	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TAAGATGGCATCTGATTTTCT	0.453													t|||	13	0.00259585	0.0	0.0043	5008	,	,		22569	0.0		0.0099	False		,,,				2504	0.0				p.S82P		Atlas-SNP	.											.	OR2L3	97	.	0			c.T244C						PASS	.	T	PRO/SER,	13,4393		0,13,2190	296.0	271.0	279.0		244,	0.6	0.0	1	dbSNP_134	279	122,8478		1,120,4179	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	74,	1,133,6369	CC,CT,TT		1.4186,0.2951,1.038	benign,	82/313,	248224227	135,12871	2203	4300	6503	SO:0001583	missense	391192	exon1			ATGGCATCTGATT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.244T>C	1.37:g.248224227T>C	ENSP00000353044:p.Ser82Pro	234.0	0.0	0		223.0	107.0	0.479821	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	.	6.953	0.545676	0.13312	0.002951	0.014186	ENSG00000198128	ENST00000359959	T	0.00402	7.56	2.05	0.632	0.17705	GPCR, rhodopsin-like superfamily (1);	0.970417	0.08347	U	0.959841	T	0.00300	0.0009	L	0.45470	1.425	0.09310	N	1	B	0.33379	0.41	B	0.42692	0.395	T	0.40270	-0.9572	10	0.37606	T	0.19	.	3.912	0.09207	0.1729:0.0:0.2867:0.5404	.	82	Q8NG85	OR2L3_HUMAN	P	82	ENSP00000353044:S82P	ENSP00000353044:S82P	S	+	1	0	OR2L3	246290850	0.000000	0.05858	0.004000	0.12327	0.072000	0.16883	-2.738000	0.00800	0.928000	0.37168	0.379000	0.24179	TCT	T|0.992;C|0.008	0.008	strong		0.453	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
PPP4R4	57718	hgsc.bcm.edu	37	14	94722815	94722815	+	Silent	SNP	G	G	A	rs114970142	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94722815G>A	ENST00000304338.3	+	17	2038	c.1884G>A	c.(1882-1884)ctG>ctA	p.L628L		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	628					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						TTTGCTACCTGTTGCCCAAAG	0.318													G|||	70	0.0139776	0.0	0.0	5008	,	,		18900	0.0188		0.0	False		,,,				2504	0.0521				p.L628L		Atlas-SNP	.											.	PPP4R4	107	.	0			c.G1884A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	85.0	89.0	87.0		1884	-3.5	0.4	14	dbSNP_132	87	0,8598		0,0,4299	no	coding-synonymous	PPP4R4	NM_058237.1		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		628/874	94722815	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	57718	exon17			CTACCTGTTGCCC	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	23788	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 14"""		"""KIAA1622"""	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1884G>A	14.37:g.94722815G>A		41.0	0.0	0		35.0	13.0	0.371429	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	37	CCDS9921.1																																																																																			G|0.989;A|0.011	0.011	strong		0.318	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237	
CHST8	64377	hgsc.bcm.edu	37	19	34262922	34262922	+	Missense_Mutation	SNP	C	C	T	rs149660944	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:34262922C>T	ENST00000262622.4	+	4	987	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	CHST8_ENST00000434302.1_Missense_Mutation_p.R77W|CHST8_ENST00000438847.3_Missense_Mutation_p.R77W	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	77			R -> W (probable disease-associated mutation found in generalized non- inflammatory peeling skin syndrome type A; results in decreased enzyme activity; the mutant protein shows reduced glycosylation; dbSNP:rs149660944). {ECO:0000269|PubMed:22289416}.		carbohydrate biosynthetic process (GO:0016051)|central nervous system development (GO:0007417)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(5)	27	Esophageal squamous(110;0.162)					GAGGGTCACTCGGGACTTATC	0.652													C|||	7	0.00139776	0.0	0.0058	5008	,	,		12973	0.0		0.003	False		,,,				2504	0.0				p.R77W		Atlas-SNP	.											.	CHST8	70	.	0			c.C229T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	3,4395	6.2+/-15.9	0,3,2196	34.0	44.0	41.0		229,229,229	4.0	0.0	19	dbSNP_134	41	62,8536	38.3+/-94.2	0,62,4237	yes	missense,missense,missense	CHST8	NM_001127895.1,NM_001127896.1,NM_022467.3	101,101,101	0,65,6433	TT,TC,CC		0.7211,0.0682,0.5002	possibly-damaging,possibly-damaging,possibly-damaging	77/425,77/425,77/425	34262922	65,12931	2199	4299	6498	SO:0001583	missense	64377	exon5			GTCACTCGGGACT	AB047801	CCDS12433.1	19q13.1	2008-02-05				ENSG00000124302		"""Sulfotransferases, membrane-bound"""	15993	protein-coding gene	gene with protein product		610190				10988300, 11001942	Standard	NM_001127895		Approved	GALNAC-4-ST1	uc002nut.4	Q9H2A9		ENST00000262622.4:c.229C>T	19.37:g.34262922C>T	ENSP00000262622:p.Arg77Trp	112.0	0.0	0		103.0	51.0	0.495146	NM_001127895	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	37	CCDS12433.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	14.66	2.600258	0.46423	6.82E-4	0.007211	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.75704	-0.96;-0.96;-0.96	5.08	4.01	0.46588	.	2.113150	0.02181	N	0.060503	T	0.57710	0.2072	N	0.24115	0.695	0.09310	N	1	P	0.51537	0.946	B	0.37422	0.249	T	0.60786	-0.7194	10	0.72032	D	0.01	-13.224	12.9913	0.58620	0.0:0.8358:0.1642:0.0	.	77	Q9H2A9	CHST8_HUMAN	W	77	ENSP00000392604:R77W;ENSP00000393879:R77W;ENSP00000262622:R77W	ENSP00000262622:R77W	R	+	1	2	CHST8	38954762	0.000000	0.05858	0.002000	0.10522	0.019000	0.09904	0.297000	0.19101	1.067000	0.40740	0.478000	0.44815	CGG	C|0.995;T|0.005	0.005	strong		0.652	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467	
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:94499797A>G	ENST00000375708.3	-	5	696	c.498T>C	c.(496-498)gaT>gaC	p.D166D	ROR2_ENST00000375715.1_Silent_p.D26D|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	166					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CGTGGTAATCATCCCTGGTAA	0.512													A|||	361	0.0720847	0.1959	0.0504	5008	,	,		16550	0.0		0.0537	False		,,,				2504	0.0133				p.D166D		Atlas-SNP	.											.	ROR2	167	.	0			c.T498C						PASS	.	A		757,3649	309.1+/-290.9	63,631,1509	80.0	73.0	75.0		498	-4.9	0.8	9	dbSNP_123	75	573,8027	153.7+/-208.1	19,535,3746	no	coding-synonymous	ROR2	NM_004560.3		82,1166,5255	GG,GA,AA		6.6628,17.1811,10.226		166/944	94499797	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	4920	exon5			GTAATCATCCCTG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.498T>C	9.37:g.94499797A>G		36.0	0.0	0		30.0	14.0	0.466667	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																			A|0.902;G|0.098	0.098	strong		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
PRRC2C	23215	hgsc.bcm.edu	37	1	171509275	171509275	+	Silent	SNP	T	T	C	rs75723046	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171509275T>C	ENST00000338920.4	+	16	2901	c.2664T>C	c.(2662-2664)gaT>gaC	p.D888D	PRRC2C_ENST00000426496.2_Silent_p.D888D|PRRC2C_ENST00000392078.3_Silent_p.D890D|PRRC2C_ENST00000367742.3_Silent_p.D890D	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	888					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ACCATACTGATGCAAATAATC	0.443													T|||	13	0.00259585	0.0008	0.0043	5008	,	,		20079	0.0		0.0089	False		,,,				2504	0.0				p.D888D		Atlas-SNP	.											.	.	.	.	0			c.T2664C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	115.0	115.0	115.0		2664	-6.5	0.0	1	dbSNP_132	115	64,8536	39.3+/-95.6	0,64,4236	no	coding-synonymous	PRRC2C	NM_015172.3		0,65,6438	CC,CT,TT		0.7442,0.0227,0.4998		888/2818	171509275	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	23215	exon16			TACTGATGCAAAT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.2664T>C	1.37:g.171509275T>C		112.0	0.0	0		100.0	44.0	0.44	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2																																																																																			T|0.997;C|0.003	0.003	strong		0.443	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
DCDC2	51473	hgsc.bcm.edu	37	6	24302049	24302049	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24302049T>G	ENST00000378454.3	-	4	752	c.451A>C	c.(451-453)Aac>Cac	p.N151H		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	151	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				GAAGCTGGGTTTATGAGGTCT	0.438																																					p.N151H		Atlas-SNP	.											.	DCDC2	53	.	0			c.A451C						PASS	.						115.0	112.0	113.0					6																	24302049		2203	4300	6503	SO:0001583	missense	51473	exon5			CTGGGTTTATGAG	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.451A>C	6.37:g.24302049T>G	ENSP00000367715:p.Asn151His	131.0	0.0	0		131.0	10.0	0.0763359	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957842	0.73902	.	.	ENSG00000146038	ENST00000378454	D	0.93019	-3.15	5.87	4.68	0.58851	Doublecortin domain (4);	0.605738	0.19684	N	0.108433	T	0.81422	0.4819	N	0.24115	0.695	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.75648	-0.3245	10	0.33940	T	0.23	-2.7516	13.3134	0.60393	0.0:0.0:0.1321:0.8679	.	151	Q9UHG0	DCDC2_HUMAN	H	151	ENSP00000367715:N151H	ENSP00000367715:N151H	N	-	1	0	DCDC2	24410028	1.000000	0.71417	0.655000	0.29622	0.997000	0.91878	4.518000	0.60510	1.119000	0.41883	0.533000	0.62120	AAC	.	.	none		0.438	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
MUC5B	727897	hgsc.bcm.edu	37	11	1272793	1272793	+	Missense_Mutation	SNP	C	C	T	rs56159668	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1272793C>T	ENST00000529681.1	+	31	14741	c.14683C>T	c.(14683-14685)Ccc>Tcc	p.P4895S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.P4898S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4895	Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTCCACGGTTCCCAGCTCGTC	0.657													C|||	18	0.00359425	0.0	0.0072	5008	,	,		18506	0.0		0.0109	False		,,,				2504	0.002				p.P4895S		Atlas-SNP	.											.	MUC5B	473	.	0			c.C14683T						PASS	.	C	SER/PRO	10,4316		0,10,2153	44.0	58.0	53.0		14683	-3.6	0.0	11	dbSNP_129	53	80,8408		0,80,4164	yes	missense	MUC5B	NM_002458.2	74	0,90,6317	TT,TC,CC		0.9425,0.2312,0.7024	benign	4895/5763	1272793	90,12724	2163	4244	6407	SO:0001583	missense	727897	exon31			ACGGTTCCCAGCT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14683C>T	11.37:g.1272793C>T	ENSP00000436812:p.Pro4895Ser	86.0	0.0	0		90.0	43.0	0.477778	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	C	3.499	-0.102189	0.06967	0.002312	0.009425	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.15834	2.39;2.57	1.82	-3.64	0.04515	.	.	.	.	.	T	0.07458	0.0188	L	0.40543	1.245	0.09310	N	1	B;B	0.34015	0.435;0.435	B;B	0.24701	0.055;0.055	T	0.10660	-1.0620	9	0.87932	D	0	.	6.4846	0.22081	0.2903:0.2746:0.4351:0.0	rs56159668;rs61745878	5217;4898	A7Y9J9;E9PBJ0	.;.	S	4895;4898;4839;4594	ENSP00000436812:P4895S;ENSP00000415793:P4898S	ENSP00000343037:P4839S	P	+	1	0	MUC5B	1229369	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-6.164000	0.00078	-1.181000	0.02730	0.485000	0.47835	CCC	C|0.992;T|0.008	0.008	strong		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZBTB16	7704	hgsc.bcm.edu	37	11	114118019	114118019	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:114118019A>G	ENST00000335953.4	+	6	2104	c.1724A>G	c.(1723-1725)gAg>gGg	p.E575G	ZBTB16_ENST00000392996.2_Missense_Mutation_p.E575G|RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000535379.1_3'UTR	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	575					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		AAACCCTACGAGTGCAATGGC	0.592																																					p.E575G		Atlas-SNP	.											.	ZBTB16	101	.	0			c.A1724G						PASS	.						100.0	79.0	86.0					11																	114118019		2201	4296	6497	SO:0001583	missense	7704	exon6			CCTACGAGTGCAA	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1724A>G	11.37:g.114118019A>G	ENSP00000338157:p.Glu575Gly	110.0	0.0	0		131.0	25.0	0.19084	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	A	33	5.276369	0.95459	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.22743	1.94;1.94	5.57	5.57	0.84162	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40619	0.1124	L	0.48877	1.53	0.58432	D	0.999995	D	0.76494	0.999	D	0.87578	0.998	T	0.12268	-1.0554	10	0.49607	T	0.09	.	15.7234	0.77732	1.0:0.0:0.0:0.0	.	575	Q05516	ZBT16_HUMAN	G	575;575;452	ENSP00000338157:E575G;ENSP00000376721:E575G	ENSP00000309507:E452G	E	+	2	0	ZBTB16	113623229	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.239000	0.95389	2.113000	0.64589	0.529000	0.55759	GAG	.	.	none		0.592	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006	
LRIG2	9860	hgsc.bcm.edu	37	1	113637308	113637308	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113637308A>G	ENST00000361127.5	+	6	932	c.734A>G	c.(733-735)aAa>aGa	p.K245R		NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	245					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		AGATCTTTGAAAATGCAGCGG	0.353																																					p.K245R		Atlas-SNP	.											.	LRIG2	67	.	0			c.A734G						PASS	.						123.0	127.0	126.0					1																	113637308		2203	4300	6503	SO:0001583	missense	9860	exon6			CTTTGAAAATGCA	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"""Immunoglobulin superfamily / I-set domain containing"""	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.734A>G	1.37:g.113637308A>G	ENSP00000355396:p.Lys245Arg	239.0	0.0	0		209.0	94.0	0.449761	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399000	0.62177	.	.	ENSG00000198799	ENST00000361127	T	0.56941	0.43	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	N	0.25094	0.71	0.49798	D	0.999822	B	0.27910	0.193	B	0.32533	0.147	T	0.14337	-1.0476	10	0.25106	T	0.35	.	16.3985	0.83631	1.0:0.0:0.0:0.0	.	245	O94898	LRIG2_HUMAN	R	245	ENSP00000355396:K245R	ENSP00000355396:K245R	K	+	2	0	LRIG2	113438831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.520000	0.81821	2.274000	0.75844	0.519000	0.50382	AAA	.	.	none		0.353	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813	
BRWD1	54014	hgsc.bcm.edu	37	21	40582823	40582823	+	Silent	SNP	C	C	T	rs75046572	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:40582823C>T	ENST00000333229.2	-	35	4260	c.3933G>A	c.(3931-3933)acG>acA	p.T1311T	BRWD1_ENST00000342449.3_Silent_p.T1311T|BRWD1_ENST00000380800.3_Silent_p.T1311T	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1311					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CAACATAGTTCGTAGCTCTGA	0.348													C|||	89	0.0177716	0.0023	0.0519	5008	,	,		18539	0.0109		0.0348	False		,,,				2504	0.0041				p.T1311T	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.G3933A						PASS	.	C	,	35,4371	39.2+/-71.8	0,35,2168	104.0	97.0	99.0		3933,3933	-4.7	0.0	21	dbSNP_131	99	378,8222	122.2+/-181.2	11,356,3933	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	11,391,6101	TT,TC,CC		4.3953,0.7944,3.1755	,	1311/2321,1311/2270	40582823	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon35			ATAGTTCGTAGCT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3933G>A	21.37:g.40582823C>T		74.0	0.0	0		116.0	74.0	0.637931	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			C|0.970;T|0.030	0.030	strong		0.348	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
CTSE	1510	hgsc.bcm.edu	37	1	206319201	206319201	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:206319201G>A	ENST00000358184.2	+	3	444	c.326G>A	c.(325-327)tGc>tAc	p.C109Y	CTSE_ENST00000432969.2_Missense_Mutation_p.C34Y|CTSE_ENST00000360218.2_Missense_Mutation_p.C109Y|CTSE_ENST00000361052.3_Missense_Mutation_p.C109Y	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	109					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			TCTGTGTACTGCACTAGCCCA	0.592																																					p.C109Y		Atlas-SNP	.											.	CTSE	72	.	0			c.G326A						PASS	.						83.0	73.0	76.0					1																	206319201		2203	4300	6503	SO:0001583	missense	1510	exon3			TGTACTGCACTAG	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.326G>A	1.37:g.206319201G>A	ENSP00000350911:p.Cys109Tyr	102.0	0.0	0		88.0	13.0	0.147727	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Missense_Mutation	SNP	ENST00000358184.2	37	CCDS1462.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397470	0.62177	.	.	ENSG00000196188	ENST00000358184;ENST00000361052;ENST00000360218;ENST00000432969	T;T;T;T	0.65916	-0.18;-0.18;0.0;-0.06	4.78	4.78	0.61160	.	0.142191	0.49916	D	0.000133	D	0.86843	0.6030	H	0.98155	4.16	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.70016	0.967;0.96;0.919	D	0.91790	0.5443	10	0.87932	D	0	.	17.9775	0.89131	0.0:0.0:1.0:0.0	.	34;109;109	B4DNU8;P14091-2;P14091-1	.;.;.	Y	109;109;109;34	ENSP00000350911:C109Y;ENSP00000354337:C109Y;ENSP00000353350:C109Y;ENSP00000394607:C34Y	ENSP00000350911:C109Y	C	+	2	0	CTSE	204485824	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	8.910000	0.92685	2.655000	0.90218	0.655000	0.94253	TGC	.	.	none		0.592	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858310	27858310	+	Silent	SNP	G	G	A	rs543379280		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27858310G>A	ENST00000359303.2	-	1	260	c.261C>T	c.(259-261)agC>agT	p.S87S	HIST1H3J_ENST00000479986.1_5'Flank|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	87					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						TCACCGCCGAGCTCTGGAAAC	0.542																																					p.S87S		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.C261T						PASS	.						56.0	56.0	56.0					6																	27858310		2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			CGCCGAGCTCTGG	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.261C>T	6.37:g.27858310G>A		93.0	0.0	0		81.0	8.0	0.0987654	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	37	CCDS4638.1																																																																																			.	.	none		0.542	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
ENPP7	339221	hgsc.bcm.edu	37	17	77709383	77709383	+	Missense_Mutation	SNP	C	C	T	rs148221256	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77709383C>T	ENST00000328313.5	+	3	1162	c.941C>T	c.(940-942)gCg>gTg	p.A314V		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			AAGAAGGAGGCGTTCCCCGAG	0.607													C|||	5	0.000998403	0.0	0.0	5008	,	,		12692	0.005		0.0	False		,,,				2504	0.0				p.A314V		Atlas-SNP	.											.	ENPP7	63	.	0			c.C941T						PASS	.						79.0	69.0	72.0					17																	77709383		2203	4300	6503	SO:0001583	missense	339221	exon3			AGGAGGCGTTCCC	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.941C>T	17.37:g.77709383C>T	ENSP00000332656:p.Ala314Val	85.0	0.0	0		73.0	23.0	0.315068	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	9.525	1.109390	0.20714	.	.	ENSG00000182156	ENST00000328313	T	0.75367	-0.93	5.16	-10.3	0.00346	Alkaline-phosphatase-like, core domain (1);	2.191760	0.03750	N	0.256410	T	0.39545	0.1082	N	0.05383	-0.06	0.09310	N	1	B	0.18310	0.027	B	0.12837	0.008	T	0.42207	-0.9465	10	0.52906	T	0.07	-0.5261	5.6555	0.17640	0.5382:0.2657:0.0617:0.1344	.	314	Q6UWV6	ENPP7_HUMAN	V	314	ENSP00000332656:A314V	ENSP00000332656:A314V	A	+	2	0	ENPP7	75323978	0.003000	0.15002	0.000000	0.03702	0.013000	0.08279	0.718000	0.25866	-2.154000	0.00792	-2.138000	0.00339	GCG	C|0.998;T|0.002	0.002	strong		0.607	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
SCML4	256380	hgsc.bcm.edu	37	6	108067907	108067907	+	Missense_Mutation	SNP	C	C	T	rs142985964	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:108067907C>T	ENST00000369020.3	-	4	718	c.473G>A	c.(472-474)gGt>gAt	p.G158D	SCML4_ENST00000479803.1_5'Flank|SCML4_ENST00000369021.3_Missense_Mutation_p.G129D|SCML4_ENST00000369022.2_Missense_Mutation_p.G100D	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CACCATCTCACCACCATAGCC	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		17701	0.0		0.002	False		,,,				2504	0.0				p.G158D		Atlas-SNP	.											.	SCML4	65	.	0			c.G473A						PASS	.	C	ASP/GLY	4,4402	6.2+/-15.9	0,4,2199	101.0	99.0	100.0		473	5.0	0.8	6	dbSNP_134	100	16,8584	11.2+/-40.8	0,16,4284	yes	missense	SCML4	NM_198081.3	94	0,20,6483	TT,TC,CC		0.186,0.0908,0.1538	probably-damaging	158/415	108067907	20,12986	2203	4300	6503	SO:0001583	missense	256380	exon4			ATCTCACCACCAT		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.473G>A	6.37:g.108067907C>T	ENSP00000358016:p.Gly158Asp	85.0	0.0	0		63.0	35.0	0.555556	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.6	4.172295	0.78452	9.08E-4	0.00186	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.98	4.98	0.66077	.	0.787668	0.12505	N	0.462982	T	0.68449	0.3002	M	0.84326	2.69	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.987;0.991	T	0.69011	-0.5258	10	0.54805	T	0.06	.	18.4486	0.90695	0.0:1.0:0.0:0.0	.	158;158;129	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	D	100;158;129;129	ENSP00000358018:G100D;ENSP00000358016:G158D;ENSP00000358017:G129D;ENSP00000404688:G129D	ENSP00000358016:G158D	G	-	2	0	SCML4	108174600	0.999000	0.42202	0.798000	0.32154	0.803000	0.45373	4.444000	0.60001	2.589000	0.87451	0.563000	0.77884	GGT	C|0.999;T|0.001	0.001	strong		0.622	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
OSGIN1	29948	hgsc.bcm.edu	37	16	83992895	83992895	+	Missense_Mutation	SNP	A	A	G	rs150635654	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:83992895A>G	ENST00000343939.2	+	4	730	c.347A>G	c.(346-348)tAc>tGc	p.Y116C	OSGIN1_ENST00000361711.3_Missense_Mutation_p.Y33C|OSGIN1_ENST00000393306.1_Missense_Mutation_p.Y33C|OSGIN1_ENST00000565123.1_Missense_Mutation_p.Y33C			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	116					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						TGCCTGTCCTACCTGCTCTCC	0.627													A|||	2	0.000399361	0.0	0.0	5008	,	,		14501	0.0		0.002	False		,,,				2504	0.0				p.Y33C		Atlas-SNP	.											.	OSGIN1	33	.	0			c.A98G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR	2,4398	4.2+/-10.8	0,2,2198	149.0	127.0	134.0		347,98,98	4.7	1.0	16	dbSNP_134	134	21,8579	16.0+/-53.3	0,21,4279	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	194,194,194	0,23,6477	GG,GA,AA		0.2442,0.0455,0.1769	probably-damaging,probably-damaging,probably-damaging	116/561,33/478,33/478	83992895	23,12977	2200	4300	6500	SO:0001583	missense	29948	exon3			TGTCCTACCTGCT	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.347A>G	16.37:g.83992895A>G	ENSP00000343376:p.Tyr116Cys	80.0	0.0	0		79.0	37.0	0.468354	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	16.64	3.178546	0.57692	4.55E-4	0.002442	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.44881	0.91;0.91;0.91	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.59838	0.2223	L	0.59436	1.845	0.54753	D	0.99998	D	0.89917	1.0	D	0.87578	0.998	T	0.63752	-0.6566	10	0.87932	D	0	-0.215	13.2677	0.60144	1.0:0.0:0.0:0.0	.	116	Q9UJX0	OSGI1_HUMAN	C	116;33;33	ENSP00000343376:Y116C;ENSP00000355374:Y33C;ENSP00000376983:Y33C	ENSP00000343376:Y116C	Y	+	2	0	OSGIN1	82550396	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	9.277000	0.95755	1.744000	0.51775	0.172000	0.16884	TAC	A|0.999;G|0.001	0.001	strong		0.627	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
ATAD2	29028	hgsc.bcm.edu	37	8	124360487	124360487	+	Silent	SNP	G	G	A	rs77106954	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124360487G>A	ENST00000287394.5	-	15	1940	c.1833C>T	c.(1831-1833)caC>caT	p.H611H	ATAD2_ENST00000521903.1_5'UTR|MIR548AA1_ENST00000384971.2_RNA	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	611					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AATCCCTGGTGTGAATCTTTA	0.284													G|||	105	0.0209665	0.0499	0.0187	5008	,	,		14148	0.001		0.0179	False		,,,				2504	0.0072				p.H611H		Atlas-SNP	.											.	ATAD2	160	.	0			c.C1833T						PASS	.	G		172,4232	103.8+/-142.4	3,166,2033	36.0	38.0	37.0		1833	1.5	1.0	8	dbSNP_132	37	174,8424	78.9+/-141.6	1,172,4126	no	coding-synonymous	ATAD2	NM_014109.3		4,338,6159	AA,AG,GG		2.0237,3.9055,2.6611		611/1391	124360487	346,12656	2202	4299	6501	SO:0001819	synonymous_variant	29028	exon15			CCTGGTGTGAATC	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1833C>T	8.37:g.124360487G>A		124.0	0.0	0		73.0	26.0	0.356164	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																			G|0.979;A|0.021	0.021	strong		0.284	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
COL27A1	85301	hgsc.bcm.edu	37	9	117029826	117029826	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:117029826G>A	ENST00000356083.3	+	34	3881	c.3490G>A	c.(3490-3492)Gcc>Acc	p.A1164T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1164	Collagen-like 9.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TCCTGGGGAAGCCGGGATGAA	0.562																																					p.A1164T		Atlas-SNP	.											.	COL27A1	200	.	0			c.G3490A						PASS	.						78.0	90.0	86.0					9																	117029826		2203	4300	6503	SO:0001583	missense	85301	exon34			GGGGAAGCCGGGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3490G>A	9.37:g.117029826G>A	ENSP00000348385:p.Ala1164Thr	53.0	0.0	0		61.0	4.0	0.0655738	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771909	0.49680	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93426	-3.22	5.22	3.18	0.36537	.	.	.	.	.	D	0.83608	0.5291	N	0.11673	0.155	0.22292	N	0.999229	B	0.30793	0.295	B	0.29267	0.1	T	0.73379	-0.4001	9	0.26408	T	0.33	.	7.4249	0.27094	0.0:0.1776:0.6234:0.199	.	1164	Q8IZC6	CORA1_HUMAN	T	1164	ENSP00000348385:A1164T	ENSP00000348385:A1164T	A	+	1	0	COL27A1	116069647	1.000000	0.71417	0.991000	0.47740	0.948000	0.59901	1.803000	0.38863	1.141000	0.42275	0.462000	0.41574	GCC	.	.	none		0.562	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
MT-ND4	4538	hgsc.bcm.edu	37	M	12088	12088	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrM:12088C>T	ENST00000361381.2	+	1	1329	c.1329C>T	c.(1327-1329)ccC>ccT	p.P443P	MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	443					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CACCTATCCCCCATTCTCCTC	0.428																																					p.P443P		Atlas-SNP	.											.	.	.	.	0			c.C1329T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ATCCCCCATTCTC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1329C>T	M.37:g.12088C>T		6.0	0.0	0		17.0	6.0	0.352941	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.428	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
POMK	84197	hgsc.bcm.edu	37	8	42977591	42977591	+	Silent	SNP	G	G	C	rs34040483	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:42977591G>C	ENST00000331373.5	+	5	879	c.624G>C	c.(622-624)ctG>ctC	p.L208L		NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|carbohydrate phosphorylation (GO:0046835)|learning or memory (GO:0007611)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|protein O-linked glycosylation (GO:0006493)|sensory perception of pain (GO:0019233)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|carbohydrate kinase activity (GO:0019200)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|protein kinase activity (GO:0004672)										CCAACGACCTGCCGAAGACAC	0.557													G|||	23	0.00459265	0.0008	0.013	5008	,	,		22021	0.0		0.0129	False		,,,				2504	0.0				p.L208L		Atlas-SNP	.											.	.	.	.	0			c.G624C						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	66.0	52.0	57.0		624	3.3	1.0	8	dbSNP_126	57	110,8490	58.3+/-119.8	1,108,4191	no	coding-synonymous	SGK196	NM_032237.3		1,116,6386	CC,CG,GG		1.2791,0.1816,0.9073		208/351	42977591	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	0	exon5			CGACCTGCCGAAG		CCDS6141.1	8p11.21	2013-08-22			ENSG00000185900	ENSG00000185900			26267	protein-coding gene	gene with protein product		615247				16879967, 23519211	Standard	NM_001277971		Approved	FLJ23356, SgK196		Q9H5K3	OTTHUMG00000164100	ENST00000331373.5:c.624G>C	8.37:g.42977591G>C		90.0	0.0	0		85.0	38.0	0.447059	NM_032237		Silent	SNP	ENST00000331373.5	37	CCDS6141.1																																																																																			G|0.992;C|0.008	0.008	strong		0.557	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377291.2	NM_032237	
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124330421C>G	ENST00000338354.3	+	4	261	c.155C>G	c.(154-156)tCg>tGg	p.S52W	DMBT1_ENST00000368909.3_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_Missense_Mutation_p.S52W|DMBT1_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	52			S -> W (in dbSNP:rs75209396). {ECO:0000269|PubMed:12185598, ECO:0000269|PubMed:12353266}.		defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCATTTCCCTCGGAGTCGACC	0.537													c|||	329	0.0656949	0.23	0.0231	5008	,	,		22102	0.001		0.007	False		,,,				2504	0.001				p.S52W	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C155G						PASS	.	C	TRP/SER,TRP/SER,TRP/SER	658,3106		51,556,1275	168.0	167.0	167.0		155,155,155	1.0	0.0	10	dbSNP_132	167	51,8185		0,51,4067	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	177,177,177	51,607,5342	GG,GC,CC		0.6192,17.4814,5.9083	probably-damaging,probably-damaging,probably-damaging	52/1786,52/2414,52/2404	124330421	709,11291	1882	4118	6000	SO:0001583	missense	1755	exon4			TTCCCTCGGAGTC		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.155C>G	10.37:g.124330421C>G	ENSP00000342210:p.Ser52Trp	161.0	0.0	0		192.0	94.0	0.489583	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		130	0.05952380952380952	118	0.23983739837398374	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	10.71	1.426167	0.25726	0.174814	0.006192	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.26223	1.85;1.84;1.78;1.85;1.84;1.78;1.75	1.9	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P;P;D	0.76494	0.997;0.572;0.922;0.529;0.999	D;B;B;B;P	0.65443	0.935;0.152;0.206;0.202;0.902	T	0.24476	-1.0159	8	0.66056	D	0.02	.	4.3987	0.11376	0.0:0.7908:0.0:0.2092	.	52;52;52;52;52	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	W	52	ENSP00000342210:S52W;ENSP00000343175:S52W;ENSP00000327747:S52W;ENSP00000357905:S52W;ENSP00000357951:S52W;ENSP00000357952:S52W;ENSP00000352593:S52W	ENSP00000331522:S52W	S	+	2	0	DMBT1	124320411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.122000	0.15687	0.337000	0.23665	0.205000	0.17691	TCG	C|0.950;G|0.050	0.050	strong		0.537	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
AIPL1	23746	hgsc.bcm.edu	37	17	6337404	6337404	+	Silent	SNP	G	G	A	rs11650007	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6337404G>A	ENST00000381129.3	-	2	191	c.111C>T	c.(109-111)ttC>ttT	p.F37F	AIPL1_ENST00000570466.1_Intron|AIPL1_ENST00000574506.1_Intron|AIPL1_ENST00000575265.1_Silent_p.F37F|AIPL1_ENST00000576776.1_Silent_p.F37F|AIPL1_ENST00000250087.5_Silent_p.F37F|AIPL1_ENST00000576307.1_Intron|AIPL1_ENST00000571740.1_Silent_p.F37F	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	37					negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		TCATGGTGCGGAAATGAAAGA	0.567													G|||	31	0.0061901	0.0	0.0043	5008	,	,		18369	0.0		0.0278	False		,,,				2504	0.0				p.F37F		Atlas-SNP	.											.	AIPL1	34	.	0			c.C111T						PASS	.	G	,,	36,4370	39.2+/-71.8	0,36,2167	118.0	83.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	111,,111	3.8	1.0	17	dbSNP_120	95	238,8362	95.0+/-156.8	1,236,4063	no	coding-synonymous,intron,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	1,272,6230	AA,AG,GG		2.7674,0.8171,2.1067	,,	37/322,,37/385	6337404	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon2			GGTGCGGAAATGA	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"""aryl hydrocarbon receptor-interacting protein-like 1"""	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.111C>T	17.37:g.6337404G>A		100.0	0.0	0		89.0	38.0	0.426966	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
SH3RF3	344558	hgsc.bcm.edu	37	2	110065896	110065896	+	Missense_Mutation	SNP	C	C	T	rs192679474	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:110065896C>T	ENST00000309415.6	+	8	2099	c.2099C>T	c.(2098-2100)tCc>tTc	p.S700F		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	700							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CTGTCCACATCCAGCCCCACC	0.597													C|||	4	0.000798722	0.0	0.0	5008	,	,		18161	0.0		0.004	False		,,,				2504	0.0				p.S700F		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C2099T						PASS	.	C	PHE/SER	8,4010		0,8,2001	38.0	43.0	41.0		2099	3.1	0.5	2		41	48,8272		0,48,4112	yes	missense	SH3RF3	NM_001099289.1	155	0,56,6113	TT,TC,CC		0.5769,0.1991,0.4539	possibly-damaging	700/883	110065896	56,12282	2009	4160	6169	SO:0001583	missense	344558	exon8			CCACATCCAGCCC	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"""RING-type (C3HC4) zinc fingers"""	24699	protein-coding gene	gene with protein product			"""SH3 multiple domains 4"""	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.2099C>T	2.37:g.110065896C>T	ENSP00000309186:p.Ser700Phe	114.0	0.0	0		97.0	42.0	0.43299	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	14.04	2.416624	0.42918	0.001991	0.005769	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.58652	0.32;2.12	4.9	3.06	0.35304	.	1.159960	0.06021	N	0.651244	T	0.49338	0.1551	.	.	.	0.23827	N	0.996736	D	0.54397	0.966	P	0.47430	0.547	T	0.39440	-0.9614	9	0.49607	T	0.09	-5.2094	8.14	0.31078	0.0:0.4772:0.4348:0.0879	.	700	Q8TEJ3	SH3R3_HUMAN	F	700	ENSP00000414997:S700F;ENSP00000309186:S700F	ENSP00000309186:S700F	S	+	2	0	SH3RF3	109432328	0.053000	0.20554	0.513000	0.27749	0.645000	0.38454	0.930000	0.28858	0.630000	0.30394	0.655000	0.94253	TCC	C|0.998;T|0.002	0.002	strong		0.597	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289	
NAALADL2	254827	hgsc.bcm.edu	37	3	174974265	174974265	+	Silent	SNP	C	C	T	rs192980349	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:174974265C>T	ENST00000454872.1	+	4	1013	c.885C>T	c.(883-885)aaC>aaT	p.N295N	NAALADL2_ENST00000473253.1_3'UTR|NAALADL2-AS2_ENST00000424690.1_RNA	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	295						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		AAATAAAAAACGTAACAAATC	0.353													T|||	2	0.000399361	0.0	0.0	5008	,	,		18334	0.0		0.002	False		,,,				2504	0.0				p.N295N		Atlas-SNP	.											.	NAALADL2	86	.	0			c.C885T						PASS	.	T		2,3672		0,2,1835	91.0	85.0	87.0		885	2.2	0.1	3		87	13,8173		0,13,4080	no	coding-synonymous	NAALADL2	NM_207015.2		0,15,5915	TT,TC,CC		0.1588,0.0544,0.1265		295/796	174974265	15,11845	1837	4093	5930	SO:0001819	synonymous_variant	254827	exon4			AAAAAACGTAACA		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.885C>T	3.37:g.174974265C>T		118.0	0.0	0		102.0	48.0	0.470588	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Silent	SNP	ENST00000454872.1	37	CCDS46960.1																																																																																			C|0.999;T|0.001	0.001	strong		0.353	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
ATG2B	55102	hgsc.bcm.edu	37	14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	rs183527316	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:96800027C>T	ENST00000359933.4	-	8	2098	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	402					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TTGCTTACCACGGCTAGAAGG	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		16337	0.0		0.002	False		,,,				2504	0.0				p.R402H		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1205A						PASS	.	C	HIS/ARG	4,3650		0,4,1823	77.0	70.0	72.0		1205	5.6	1.0	14		72	59,8131		0,59,4036	yes	missense	ATG2B	NM_018036.5	29	0,63,5859	TT,TC,CC		0.7204,0.1095,0.5319	benign	402/2079	96800027	63,11781	1827	4095	5922	SO:0001583	missense	55102	exon8			TTACCACGGCTAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1205G>A	14.37:g.96800027C>T	ENSP00000353010:p.Arg402His	81.0	0.0	0		98.0	50.0	0.510204	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.68	3.189548	0.57909	0.001095	0.007204	ENSG00000066739	ENST00000359933	T	0.10382	2.88	5.6	5.6	0.85130	.	0.423584	0.20315	U	0.094755	T	0.05640	0.0148	N	0.19112	0.55	0.47341	D	0.999394	B	0.22211	0.066	B	0.14023	0.01	T	0.24657	-1.0154	10	0.41790	T	0.15	.	13.2187	0.59875	0.0:0.9272:0.0:0.0728	.	402	Q96BY7	ATG2B_HUMAN	H	402	ENSP00000353010:R402H	ENSP00000353010:R402H	R	-	2	0	ATG2B	95869780	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.238000	0.65366	2.793000	0.96121	0.591000	0.81541	CGT	C|0.998;T|0.002	0.002	strong		0.363	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662851	7662851	+	Splice_Site	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7662851A>C	ENST00000299492.4	+	16	1905	c.1517A>C	c.(1516-1518)aAa>aCa	p.K506T	PPFIBP2_ENST00000530181.1_Splice_Site_p.K363T|PPFIBP2_ENST00000533792.1_Splice_Site_p.K348T|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Splice_Site_p.K394T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	506					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TTCTGGGGAAAGTAAGTTGGT	0.438																																					p.K506T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.A1517C						PASS	.						133.0	120.0	125.0					11																	7662851		2201	4296	6497	SO:0001630	splice_region_variant	8495	exon16			GGGGAAAGTAAGT	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1517+1A>C	11.37:g.7662851A>C		94.0	0.0	0		92.0	24.0	0.26087	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.70|18.70	3.680571|3.680571	0.68042|0.68042	.|.	.|.	ENSG00000166387|ENSG00000166387	ENST00000534409|ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000530081	.|T;T;T;T	.|0.48836	.|1.23;0.81;1.23;0.8	6.03|6.03	4.91|4.91	0.64330|0.64330	.|.	0.063724|0.063724	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.60945|0.60945	0.2308|0.2308	L|L	0.59436|0.59436	1.845|1.845	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D;D	.|0.76494	.|0.998;0.995;0.999;0.998;0.998;0.998	.|D;P;D;P;P;D	.|0.78314	.|0.931;0.844;0.991;0.898;0.898;0.98	T|T	0.62623|0.62623	-0.6815|-0.6815	6|10	.|0.87932	.|D	.|0	-15.9732|-15.9732	7.7136|7.7136	0.28692|0.28692	0.8399:0.0:0.1601:0.0|0.8399:0.0:0.1601:0.0	.|.	.|394;394;429;348;363;506	.|E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.|.;.;.;.;.;LIPB2_HUMAN	N|T	196|506;348;348;429;394;363;167	.|ENSP00000299492:K506T;ENSP00000436498:K348T;ENSP00000435469:K394T;ENSP00000437321:K363T	.|ENSP00000299492:K506T	K|K	+|+	3|2	2|0	PPFIBP2|PPFIBP2	7619427|7619427	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	3.973000|3.973000	0.56845|0.56845	1.102000|1.102000	0.41551|0.41551	0.533000|0.533000	0.62120|0.62120	AAA|AAA	.	.	none		0.438	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	Missense_Mutation
HIST2H3D	653604	hgsc.bcm.edu	37	1	149784843	149784843	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149784843G>A	ENST00000331491.1	-	1	393	c.394C>T	c.(394-396)Cgc>Tgc	p.R132C	HIST2H2BF_ENST00000469483.1_5'Flank|HIST2H2BF_ENST00000369167.1_5'Flank|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000545683.1_5'Flank|HIST2H2BF_ENST00000427880.2_5'Flank	NM_001123375.2	NP_001116847.1	Q71DI3	H32_HUMAN	histone cluster 2, H3d	132					blood coagulation (GO:0007596)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			biliary_tract(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(3)	7						CGCTCCCCGCGGATGCGGCGG	0.577																																					p.R132C		Atlas-SNP	.											.	HIST2H3D	15	.	0			c.C394T						PASS	.						57.0	60.0	59.0					1																	149784843		1567	3581	5148	SO:0001583	missense	653604	exon1			CCCCGCGGATGCG	AL591493	CCDS41388.1	1q21.2	2012-03-08	2006-10-11		ENSG00000183598	ENSG00000183598		"""Histones / Replication-dependent"""	25311	protein-coding gene	gene with protein product			"""histone 2, H3d"""				Standard	NM_001123375		Approved		uc010pbl.2	Q71DI3	OTTHUMG00000012092	ENST00000331491.1:c.394C>T	1.37:g.149784843G>A	ENSP00000333277:p.Arg132Cys	239.0	0.0	0		238.0	15.0	0.0630252	NM_001123375	A2BDF6|A6NFS4|Q6B053	Missense_Mutation	SNP	ENST00000331491.1	37	CCDS41388.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.590096	0.66105	.	.	ENSG00000183598	ENST00000331491	T	0.70164	-0.46	4.04	4.04	0.47022	.	0.000000	0.53938	U	0.000041	T	0.71187	0.3310	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74278	-0.3717	7	0.52906	T	0.07	.	15.2971	0.73916	0.0:0.0:1.0:0.0	.	.	.	.	C	132	ENSP00000333277:R132C	ENSP00000333277:R132C	R	-	1	0	HIST2H3D	148051467	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.027000	0.76463	2.262000	0.75019	0.436000	0.28706	CGC	.	.	none		0.577	HIST2H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033452.1	NM_001123375	
MYO7B	4648	hgsc.bcm.edu	37	2	128367451	128367451	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:128367451C>T	ENST00000409816.2	+	23	3084	c.3052C>T	c.(3052-3054)Ctg>Ttg	p.L1018L	MYO7B_ENST00000428314.1_Silent_p.L1018L|MYO7B_ENST00000389524.4_Silent_p.L1018L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1018	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GAACGTCATCCTGAGGTTCAT	0.597																																					p.L1018L		Atlas-SNP	.											.	MYO7B	359	.	0			c.C3052T						PASS	.						45.0	49.0	48.0					2																	128367451		2091	4242	6333	SO:0001819	synonymous_variant	4648	exon24			GTCATCCTGAGGT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3052C>T	2.37:g.128367451C>T		177.0	0.0	0		116.0	13.0	0.112069	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			.	.	none		0.597	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SGK1	6446	hgsc.bcm.edu	37	6	134495218	134495218	+	Splice_Site	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495218G>A	ENST00000237305.7	-	3	241	c.153C>T	c.(151-153)caC>caT	p.H51H	SGK1_ENST00000528577.1_Splice_Site_p.H79H|SGK1_ENST00000413996.3_Splice_Site_p.H65H|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Splice_Site_p.H41H|SGK1_ENST00000475719.2_Splice_Site_p.H51H|SGK1_ENST00000367858.5_Splice_Site_p.H146H	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	51	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GAACTTCAGGGCTGCAGGGAA	0.498																																					p.H146H		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.C438T						PASS	.						111.0	104.0	107.0					6																	134495218		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon5			TTCAGGGCTGCAG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.153-1C>T	6.37:g.134495218G>A		62.0	0.0	0		70.0	21.0	0.3	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.498	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Silent
TTC12	54970	hgsc.bcm.edu	37	11	113234603	113234603	+	Silent	SNP	G	G	A	rs34940277	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113234603G>A	ENST00000529221.1	+	20	1875	c.1770G>A	c.(1768-1770)acG>acA	p.T590T	TTC12_ENST00000314756.3_Silent_p.T590T|TTC12_ENST00000393020.1_Silent_p.T590T|TTC12_ENST00000483239.2_Silent_p.T596T	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	590										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		CTATCTGCACGAATAGTTATC	0.388													G|||	8	0.00159744	0.0	0.0	5008	,	,		22890	0.002		0.002	False		,,,				2504	0.0041				p.T590T		Atlas-SNP	.											.	TTC12	66	.	0			c.G1770A						PASS	.	G		2,4400	4.2+/-10.8	0,2,2199	125.0	116.0	119.0		1770	-11.2	0.0	11	dbSNP_126	119	9,8583	7.1+/-27.0	0,9,4287	no	coding-synonymous	TTC12	NM_017868.3		0,11,6486	AA,AG,GG		0.1047,0.0454,0.0847		590/706	113234603	11,12983	2201	4296	6497	SO:0001819	synonymous_variant	54970	exon20			CTGCACGAATAGT	AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.1770G>A	11.37:g.113234603G>A		89.0	0.0	0		94.0	74.0	0.787234	NM_017868	Q8N5H9|Q9NWY3	Silent	SNP	ENST00000529221.1	37	CCDS8360.2																																																																																			G|0.999;A|0.001	0.001	strong		0.388	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
MTUS1	57509	hgsc.bcm.edu	37	8	17532715	17532715	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17532715A>C	ENST00000262102.6	-	8	3109	c.2885T>G	c.(2884-2886)gTt>gGt	p.V962G	MTUS1_ENST00000519263.1_Missense_Mutation_p.V908G|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000297488.6_Missense_Mutation_p.V128G|MTUS1_ENST00000544260.1_Missense_Mutation_p.V107G|MTUS1_ENST00000381869.3_Missense_Mutation_p.V908G|MTUS1_ENST00000381861.3_Missense_Mutation_p.V209G|MTUS1_ENST00000400046.1_Missense_Mutation_p.V34G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	962					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CCGGAGGTTAACAAGTTCTTG	0.443																																					p.V962G		Atlas-SNP	.											.	MTUS1	144	.	0			c.T2885G						PASS	.						205.0	188.0	194.0					8																	17532715		1932	4128	6060	SO:0001583	missense	57509	exon8			AGGTTAACAAGTT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2885T>G	8.37:g.17532715A>C	ENSP00000262102:p.Val962Gly	92.0	0.0	0		128.0	27.0	0.210938	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.976972	0.53720	.	.	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.36699	1.24;1.24;2.14;1.24;1.24;1.24;1.24	4.61	4.61	0.57282	.	0.674999	0.14765	N	0.299724	T	0.37517	0.1006	L	0.35487	1.065	0.58432	D	0.999997	B;B;B;B	0.29646	0.043;0.253;0.141;0.231	B;B;B;B	0.41202	0.191;0.35;0.191;0.1	T	0.18053	-1.0349	10	0.32370	T	0.25	-7.869	14.5445	0.68017	1.0:0.0:0.0:0.0	.	908;962;209;128	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	908;107;34;128;209;962;908	ENSP00000371293:V908G;ENSP00000445738:V107G;ENSP00000382921:V34G;ENSP00000297488:V128G;ENSP00000371285:V209G;ENSP00000262102:V962G;ENSP00000430167:V908G	ENSP00000262102:V962G	V	-	2	0	MTUS1	17576995	0.133000	0.22466	0.969000	0.41365	0.996000	0.88848	3.829000	0.55760	2.083000	0.62718	0.378000	0.23410	GTT	.	.	none		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
EPPK1	83481	hgsc.bcm.edu	37	8	144947062	144947062	+	Silent	SNP	C	C	T	rs7819087	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144947062C>T	ENST00000525985.1	-	2	431	c.360G>A	c.(358-360)acG>acA	p.T120T				P58107	EPIPL_HUMAN	epiplakin 1	120						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGATAGCCCGTAGTGGCAC	0.677													C|||	150	0.0299521	0.1067	0.0101	5008	,	,		19734	0.0		0.002	False		,,,				2504	0.0				p.T120T		Atlas-SNP	.											.	EPPK1	199	.	0			c.G360A						PASS	.	C		277,3819		11,255,1782	27.0	33.0	31.0		360	-2.5	0.6	8	dbSNP_116	31	10,8366		0,10,4178	no	coding-synonymous	EPPK1	NM_031308.1		11,265,5960	TT,TC,CC		0.1194,6.7627,2.3012		120/2420	144947062	287,12185	2048	4188	6236	SO:0001819	synonymous_variant	83481	exon1			ATAGCCCGTAGTG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.360G>A	8.37:g.144947062C>T		123.0	0.0	0		113.0	70.0	0.619469	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.955;T|0.045	0.045	strong		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ZFP2	80108	hgsc.bcm.edu	37	5	178359075	178359075	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178359075G>C	ENST00000361362.2	+	5	1291	c.761G>C	c.(760-762)aGc>aCc	p.S254T	ZFP2_ENST00000503510.2_Missense_Mutation_p.S254T|ZFP2_ENST00000523286.1_Missense_Mutation_p.S254T|ZFP2_ENST00000520301.1_Missense_Mutation_p.S254T	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	254					regulation of transcription, DNA-templated (GO:0006355)|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)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		TTCAGTCAAAGCATGCATCTT	0.383																																					p.S254T		Atlas-SNP	.											.	ZFP2	70	.	0			c.G761C						PASS	.						68.0	71.0	70.0					5																	178359075		2203	4300	6503	SO:0001583	missense	80108	exon5			GTCAAAGCATGCA	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"""Zinc fingers, C2H2-type"""	26138	protein-coding gene	gene with protein product			"""zinc finger protein 2 homolog (mouse)"""				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.761G>C	5.37:g.178359075G>C	ENSP00000354453:p.Ser254Thr	27.0	0.0	0		44.0	17.0	0.386364	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	g	6.700	0.497745	0.12762	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	4.67	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38111	N	0.001818	T	0.11024	0.0269	M	0.74389	2.26	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.10132	-1.0643	10	0.33141	T	0.24	-5.845	8.6489	0.34022	0.1014:0.0:0.8986:0.0	.	254	Q6ZN57	ZFP2_HUMAN	T	254	ENSP00000354453:S254T;ENSP00000430980:S254T;ENSP00000430531:S254T;ENSP00000438114:S254T	ENSP00000354453:S254T	S	+	2	0	ZFP2	178291681	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	0.566000	0.23593	2.408000	0.81797	0.650000	0.86243	AGC	.	.	none		0.383	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613	
EPPK1	83481	hgsc.bcm.edu	37	8	144941940	144941940	+	Silent	SNP	G	G	A	rs73715514	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144941940G>A	ENST00000525985.1	-	2	5553	c.5482C>T	c.(5482-5484)Ctg>Ttg	p.L1828L				P58107	EPIPL_HUMAN	epiplakin 1	1828						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ATGATTTCCAGCAATTTCTCC	0.537													G|||	314	0.0626997	0.2239	0.0202	5008	,	,		18564	0.0		0.004	False		,,,				2504	0.0				p.L1828L		Atlas-SNP	.											.	EPPK1	199	.	0			c.C5482T						PASS	.	G		691,3381		58,575,1403	233.0	230.0	231.0		5482	-6.8	0.0	8	dbSNP_130	231	18,8370		0,18,4176	no	coding-synonymous	EPPK1	NM_031308.1		58,593,5579	AA,AG,GG		0.2146,16.9695,5.6902		1828/2420	144941940	709,11751	2036	4194	6230	SO:0001819	synonymous_variant	83481	exon1			TTTCCAGCAATTT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5482C>T	8.37:g.144941940G>A		112.0	0.0	0		117.0	58.0	0.495726	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.951;A|0.049	0.049	strong		0.537	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
BRINP3	339479	hgsc.bcm.edu	37	1	190067970	190067970	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:190067970T>G	ENST00000367462.3	-	8	1710	c.1479A>C	c.(1477-1479)caA>caC	p.Q493H	BRINP3_ENST00000534846.1_Missense_Mutation_p.Q391H	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	493					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TCTCGAGATCTTGCAGGTCAG	0.502																																					p.Q493H		Atlas-SNP	.											FAM5C,colon,carcinoma,-2,1	FAM5C	343	1	0			c.A1479C						PASS	.						163.0	160.0	161.0					1																	190067970		2203	4300	6503	SO:0001583	missense	339479	exon8			GAGATCTTGCAGG	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1479A>C	1.37:g.190067970T>G	ENSP00000356432:p.Gln493His	96.0	0.0	0		135.0	35.0	0.259259	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.814998	0.50527	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.53423	0.62;0.62	5.75	-1.39	0.08997	.	0.000000	0.85682	D	0.000000	T	0.43567	0.1253	M	0.72894	2.215	0.49483	D	0.999797	B;B	0.28713	0.22;0.064	B;B	0.29267	0.1;0.018	T	0.44314	-0.9336	10	0.87932	D	0	.	10.6986	0.45913	0.0:0.5576:0.0:0.4424	.	391;493	B7Z260;Q76B58	.;FAM5C_HUMAN	H	493;391	ENSP00000356432:Q493H;ENSP00000438022:Q391H	ENSP00000356432:Q493H	Q	-	3	2	FAM5C	188334593	0.721000	0.28007	0.997000	0.53966	0.996000	0.88848	-0.076000	0.11412	-0.178000	0.10672	0.482000	0.46254	CAA	.	.	none		0.502	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051	
ASIP	434	hgsc.bcm.edu	37	20	32856838	32856838	+	Silent	SNP	C	C	A	rs36093428	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32856838C>A	ENST00000568305.1	+	4	466	c.264C>A	c.(262-264)ccC>ccA	p.P88P	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Silent_p.P88P			P42127	ASIP_HUMAN	agouti signaling protein	88					adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						CCCGGACCCCCCTATCTGCGC	0.706													C|||	31	0.0061901	0.0008	0.0144	5008	,	,		11685	0.0		0.0199	False		,,,				2504	0.0				p.P88P		Atlas-SNP	.											.	ASIP	6	.	0			c.C264A						PASS	.	C		3,4325		0,3,2161	9.0	11.0	11.0		264	-1.8	0.0	20	dbSNP_126	11	48,8490		0,48,4221	no	coding-synonymous	ASIP	NM_001672.2		0,51,6382	AA,AC,CC		0.5622,0.0693,0.3964		88/133	32856838	51,12815	2164	4269	6433	SO:0001819	synonymous_variant	434	exon3			GACCCCCCTATCT		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"""nonagouti homolog (mouse)"""	600201	"""agouti (mouse)-signaling protein"", ""agouti signaling protein, nonagouti homolog (mouse)"""	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.264C>A	20.37:g.32856838C>A		62.0	0.0	0		53.0	35.0	0.660377	NM_001672	Q3SXL2	Silent	SNP	ENST00000568305.1	37	CCDS13232.1																																																																																			C|0.994;A|0.006	0.006	strong		0.706	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		
CCR2	729230	hgsc.bcm.edu	37	3	46399581	46399581	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46399581A>C	ENST00000400888.2	+	1	602	c.563A>C	c.(562-564)tAt>tCt	p.Y188S	CCR2_ENST00000292301.4_Missense_Mutation_p.Y188S|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.Y188S			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	188					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		GATTCTGTTTATGTCTGTGGC	0.463																																					p.Y188S		Atlas-SNP	.											.	CCR2	103	.	0			c.A563C						PASS	.						282.0	271.0	274.0					3																	46399581		1568	3582	5150	SO:0001583	missense	729230	exon2			CTGTTTATGTCTG		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.563A>C	3.37:g.46399581A>C	ENSP00000383681:p.Tyr188Ser	168.0	0.0	0		143.0	51.0	0.356643	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	A	4.000	-0.002637	0.07819	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000400888	T;T;T	0.36878	1.23;1.23;1.23	5.04	-1.23	0.09465	GPCR, rhodopsin-like superfamily (1);	1.456690	0.04308	N	0.348450	T	0.36663	0.0975	M	0.70108	2.13	0.09310	N	1	B;B	0.23128	0.08;0.012	B;B	0.32022	0.139;0.014	T	0.36114	-0.9761	10	0.48119	T	0.1	.	0.2076	0.00152	0.3403:0.2277:0.1565:0.2756	.	188;188	P41597;Q4VBL2	CCR2_HUMAN;.	S	188	ENSP00000399285:Y188S;ENSP00000292301:Y188S;ENSP00000383681:Y188S	ENSP00000292301:Y188S	Y	+	2	0	CCR2	46374585	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.595000	0.05727	-0.382000	0.07870	0.528000	0.53228	TAT	.	.	none		0.463	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
SOX5	6660	hgsc.bcm.edu	37	12	23757393	23757393	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:23757393G>T	ENST00000451604.2	-	9	1193	c.1092C>A	c.(1090-1092)aaC>aaA	p.N364K	SOX5_ENST00000381381.2_Missense_Mutation_p.N351K|SOX5_ENST00000541536.1_Missense_Mutation_p.N351K|SOX5_ENST00000537393.1_Missense_Mutation_p.N329K|SOX5_ENST00000309359.1_Missense_Mutation_p.N351K|SOX5_ENST00000546136.1_Missense_Mutation_p.N351K|SOX5_ENST00000545921.1_Missense_Mutation_p.N354K			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	364					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						CAGCACCAAGGTTGCCTTGGG	0.512																																					p.N364K		Atlas-SNP	.											.	SOX5	134	.	0			c.C1092A						PASS	.						149.0	123.0	132.0					12																	23757393		2203	4300	6503	SO:0001583	missense	6660	exon9			ACCAAGGTTGCCT	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1092C>A	12.37:g.23757393G>T	ENSP00000398273:p.Asn364Lys	137.0	0.0	0		124.0	9.0	0.0725806	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.589489	0.86851	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.97279	-4.31;-4.31;-4.2;-4.32;-4.32;-4.2;-4.32	6.16	5.27	0.74061	.	0.443696	0.27831	N	0.017669	D	0.97816	0.9283	M	0.68593	2.085	0.80722	D	1	B;D;B	0.54772	0.321;0.968;0.399	B;D;B	0.70487	0.205;0.969;0.206	D	0.96571	0.9423	10	0.33141	T	0.24	.	14.9931	0.71406	0.0674:0.0:0.9326:0.0	.	329;351;364	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	K	351;351;351;364;316;329;351;354	ENSP00000437487:N351K;ENSP00000308927:N351K;ENSP00000370788:N351K;ENSP00000398273:N364K;ENSP00000439832:N329K;ENSP00000441973:N351K;ENSP00000443520:N354K	ENSP00000308927:N351K	N	-	3	2	SOX5	23648660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.733000	0.74796	2.937000	0.99478	0.650000	0.86243	AAC	.	.	none		0.512	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940	
GCH1	2643	hgsc.bcm.edu	37	14	55369053	55369053	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:55369053T>C	ENST00000491895.2	-	1	517	c.329A>G	c.(328-330)cAg>cGg	p.Q110R	GCH1_ENST00000543643.2_Missense_Mutation_p.Q110R|GCH1_ENST00000536224.2_Missense_Mutation_p.Q110R|GCH1_ENST00000395514.1_Missense_Mutation_p.Q110R|GCH1_ENST00000254299.4_5'UTR	NM_000161.2	NP_000152.1	P30793	GCH1_HUMAN	GTP cyclohydrolase 1	110					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|dopamine biosynthetic process (GO:0042416)|GTP catabolic process (GO:0006184)|metabolic process (GO:0008152)|negative regulation of blood pressure (GO:0045776)|neuromuscular process controlling posture (GO:0050884)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric-oxide synthase activity (GO:0051000)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|pteridine-containing compound biosynthetic process (GO:0042559)|regulation of blood pressure (GO:0008217)|regulation of lung blood pressure (GO:0014916)|regulation of nitric-oxide synthase activity (GO:0050999)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to pain (GO:0048265)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)|tetrahydrofolate biosynthetic process (GO:0046654)|vasodilation (GO:0042311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|coenzyme binding (GO:0050662)|GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(2)|lung(7)|skin(2)	11						GATGGTCTCCTGGTAGCCCTT	0.692																																					p.Q110R	Pancreas(198;1245 2204 4807 21567 38372)	Atlas-SNP	.											.	GCH1	16	.	0			c.A329G						PASS	.						21.0	23.0	23.0					14																	55369053		2203	4300	6503	SO:0001583	missense	2643	exon1			GTCTCCTGGTAGC	U19523	CCDS9720.1, CCDS41954.1, CCDS45110.1	14q22.1-q22.2	2014-04-01	2008-08-01		ENSG00000131979	ENSG00000131979	3.5.4.16		4193	protein-coding gene	gene with protein product	"""dopa-responsive dystonia"""	600225	"""dystonia 14"""	GCH, DYT5, DYT14		7874165, 8695054	Standard	XM_005267530		Approved	GTPCH1, DYT5a	uc001xbi.1	P30793	OTTHUMG00000029754	ENST00000491895.2:c.329A>G	14.37:g.55369053T>C	ENSP00000419045:p.Gln110Arg	40.0	0.0	0		41.0	15.0	0.365854	NM_000161	Q6FHY7|Q9Y4I8	Missense_Mutation	SNP	ENST00000491895.2	37	CCDS9720.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270301	0.59540	.	.	ENSG00000131979	ENST00000395514;ENST00000543643;ENST00000491895;ENST00000536224;ENST00000395524	D;D;D;D	0.99701	-6.45;-6.45;-6.45;-6.45	4.46	4.46	0.54185	.	0.116646	0.64402	D	0.000012	D	0.97945	0.9324	N	0.16166	0.38	0.80722	D	1	B;B;B;B	0.19445	0.036;0.013;0.018;0.007	B;B;B;B	0.17979	0.02;0.02;0.02;0.005	D	0.97786	1.0235	10	0.42905	T	0.14	.	12.689	0.56964	0.0:0.0:0.0:1.0	.	110;110;110;110	F8W9F6;P30793-2;P30793-4;P30793	.;.;.;GCH1_HUMAN	R	110	ENSP00000378890:Q110R;ENSP00000444011:Q110R;ENSP00000419045:Q110R;ENSP00000445246:Q110R	ENSP00000378890:Q110R	Q	-	2	0	GCH1	54438803	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.735000	0.62051	1.858000	0.53909	0.459000	0.35465	CAG	.	.	none		0.692	GCH1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276895.3		
DNAJA2	10294	hgsc.bcm.edu	37	16	47007480	47007480	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:47007480C>T	ENST00000317089.5	-	1	219	c.4G>A	c.(4-6)Gct>Act	p.A2T	RP11-169E6.1_ENST00000562536.1_RNA	NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	2					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				GCCACGTTAGCCATGGCGGCC	0.711																																					p.A2T		Atlas-SNP	.											.	DNAJA2	28	.	0			c.G4A						PASS	.						23.0	26.0	25.0					16																	47007480		2188	4272	6460	SO:0001583	missense	10294	exon1			CGTTAGCCATGGC	AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"""Heat shock proteins / DNAJ (HSP40)"""	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.4G>A	16.37:g.47007480C>T	ENSP00000314030:p.Ala2Thr	39.0	0.0	0		40.0	11.0	0.275	NM_005880	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	37	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845639	0.71603	.	.	ENSG00000069345	ENST00000317089	T	0.38560	1.13	5.07	5.07	0.68467	.	0.124512	0.53938	D	0.000052	T	0.24699	0.0599	N	0.12746	0.255	0.48975	D	0.999737	B	0.18013	0.025	B	0.20767	0.031	T	0.09079	-1.0691	10	0.18276	T	0.48	-7.404	12.3249	0.55005	0.1696:0.8304:0.0:0.0	.	2	O60884	DNJA2_HUMAN	T	2	ENSP00000314030:A2T	ENSP00000314030:A2T	A	-	1	0	DNAJA2	45564981	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	2.429000	0.44758	2.327000	0.79052	0.491000	0.48974	GCT	.	.	none		0.711	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2		
OR1L3	26735	hgsc.bcm.edu	37	9	125437664	125437664	+	Missense_Mutation	SNP	T	T	G	rs56304399	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125437664T>G	ENST00000304820.2	+	1	350	c.256T>G	c.(256-258)Tta>Gta	p.L86V		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						CGTGAACTTCTTATCAGAGAA	0.403													T|||	19	0.00379393	0.0015	0.0072	5008	,	,		24153	0.0		0.0119	False		,,,				2504	0.0				p.L86V		Atlas-SNP	.											.	OR1L3	51	.	0			c.T256G						PASS	.	T	VAL/LEU	6,4400	11.4+/-27.6	0,6,2197	161.0	159.0	160.0		256	-2.4	0.4	9	dbSNP_129	160	82,8518	48.1+/-107.5	2,78,4220	yes	missense	OR1L3	NM_001005234.1	32	2,84,6417	GG,GT,TT		0.9535,0.1362,0.6766	probably-damaging	86/325	125437664	88,12918	2203	4300	6503	SO:0001583	missense	26735	exon1			AACTTCTTATCAG		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"""GPCR / Class A : Olfactory receptors"""	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.256T>G	9.37:g.125437664T>G	ENSP00000302863:p.Leu86Val	124.0	0.0	0		132.0	72.0	0.545455	NM_001005234	B2RNF4|Q6IFN1	Missense_Mutation	SNP	ENST00000304820.2	37	CCDS35128.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	T	13.22	2.171475	0.38315	0.001362	0.009535	ENSG00000171481	ENST00000304820	T	0.10288	2.89	4.54	-2.43	0.06522	GPCR, rhodopsin-like superfamily (1);	0.286366	0.17522	U	0.171239	T	0.08802	0.0218	L	0.39898	1.24	0.09310	N	1	D	0.61697	0.99	D	0.63381	0.914	T	0.19647	-1.0299	10	0.22109	T	0.4	-5.4795	1.9974	0.03459	0.1313:0.3675:0.2093:0.2919	rs56304399	86	Q8NH93	OR1L3_HUMAN	V	86	ENSP00000302863:L86V	ENSP00000302863:L86V	L	+	1	2	OR1L3	124477485	0.000000	0.05858	0.360000	0.25837	0.990000	0.78478	-0.099000	0.11007	-0.170000	0.10816	0.524000	0.50904	TTA	T|0.993;G|0.007	0.007	strong		0.403	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1		
HRC	3270	hgsc.bcm.edu	37	19	49658345	49658345	+	Silent	SNP	G	G	A	rs117942355	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49658345G>A	ENST00000252825.4	-	1	336	c.150C>T	c.(148-150)tcC>tcT	p.S50S	TRPM4_ENST00000427978.2_5'Flank|TRPM4_ENST00000355712.5_5'Flank|TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Silent_p.S50S	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	50					cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		ATGCCTCCTCGGAGAGCCCGG	0.597													g|||	2	0.000399361	0.0	0.0014	5008	,	,		17990	0.001		0.0	False		,,,				2504	0.0				p.S50S	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C150T						PASS	.	A		0,4406		0,0,2203	147.0	132.0	137.0		150	-4.7	0.0	19	dbSNP_132	137	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	HRC	NM_002152.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		50/700	49658345	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCGGAGAGC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.150C>T	19.37:g.49658345G>A		67.0	0.0	0		61.0	27.0	0.442623	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|1.000;A|0.000	0.000	strong		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
KIF5B	3799	hgsc.bcm.edu	37	10	32320002	32320002	+	Splice_Site	SNP	G	G	A	rs35441986	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:32320002G>A	ENST00000302418.4	-	14	2037	c.1580C>T	c.(1579-1581)tCg>tTg	p.S527L		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	527					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				ATATCCTACCGATTTCTGATT	0.294			T	"""RET, ALK"""	NSCLC								G|||	2	0.000399361	0.0	0.0	5008	,	,		18252	0.0		0.002	False		,,,				2504	0.0				p.S527L		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.C1580T						PASS	.	G	LEU/SER	3,4403	4.2+/-10.8	0,3,2200	72.0	71.0	71.0		1580	6.0	1.0	10	dbSNP_126	71	31,8569	21.0+/-64.5	0,31,4269	yes	missense-near-splice	KIF5B	NM_004521.2	145	0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614	benign	527/964	32320002	34,12972	2203	4300	6503	SO:0001630	splice_region_variant	3799	exon14			CCTACCGATTTCT	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"""Kinesins"""	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1581+1C>T	10.37:g.32320002G>A		83.0	0.0	0		79.0	44.0	0.556962	NM_004521	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.33	3.807250	0.70797	6.81E-4	0.003605	ENSG00000170759	ENST00000302418	D	0.86694	-2.16	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.81370	0.4808	N	0.20685	0.6	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.73329	-0.4017	10	0.40728	T	0.16	.	20.5948	0.99439	0.0:0.0:1.0:0.0	rs35441986	527	P33176	KINH_HUMAN	L	527	ENSP00000307078:S527L	ENSP00000307078:S527L	S	-	2	0	KIF5B	32360008	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.018000	0.88722	2.873000	0.98535	0.563000	0.77884	TCG	G|0.998;A|0.002	0.002	strong		0.294	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	Missense_Mutation
COL12A1	1303	hgsc.bcm.edu	37	6	75827165	75827165	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:75827165G>A	ENST00000322507.8	-	47	7761	c.7452C>T	c.(7450-7452)gaC>gaT	p.D2484D	COL12A1_ENST00000483888.2_Silent_p.D2484D|COL12A1_ENST00000416123.2_Silent_p.D2484D|COL12A1_ENST00000345356.6_Silent_p.D1320D	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2484	Nonhelical region (NC3).|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.D2484E(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATTCAAAGTCGTCCACAATGA	0.423																																					p.D2484D		Atlas-SNP	.											COL12A1,NS,carcinoma,0,1	COL12A1	385	1	1	Substitution - Missense(1)	lung(1)	c.C7452T						PASS	.						120.0	118.0	119.0					6																	75827165		1968	4174	6142	SO:0001819	synonymous_variant	1303	exon47			AAAGTCGTCCACA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.7452C>T	6.37:g.75827165G>A		98.0	0.0	0		67.0	22.0	0.328358	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																			.	.	none		0.423	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
ALDH9A1	223	hgsc.bcm.edu	37	1	165638577	165638577	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165638577T>G	ENST00000354775.4	-	7	1345	c.1041A>C	c.(1039-1041)gaA>gaC	p.E347D	ALDH9A1_ENST00000538148.1_Missense_Mutation_p.E253D	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	323					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TCCTTGTATCTTCCAGAAGGG	0.438																																					p.E347D	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.A1041C						PASS	.						147.0	139.0	142.0					1																	165638577		2203	4300	6503	SO:0001583	missense	223	exon7			TGTATCTTCCAGA	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.1041A>C	1.37:g.165638577T>G	ENSP00000346827:p.Glu347Asp	200.0	0.0	0		201.0	69.0	0.343284	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	T	10.86	1.468997	0.26335	.	.	ENSG00000143149	ENST00000354775;ENST00000538148	T;T	0.77750	-1.12;-1.12	5.05	2.67	0.31697	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.095319	0.64402	N	0.000001	T	0.37320	0.0999	N	0.20986	0.625	0.44843	D	0.997857	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.04495	-1.0947	9	0.23302	T	0.38	.	4.2403	0.10645	0.0:0.1805:0.1747:0.6448	.	253;337;323;347	B4DYY1;B4DX14;P49189;B9EKV4	.;.;AL9A1_HUMAN;.	D	347;253	ENSP00000346827:E347D;ENSP00000440026:E253D	ENSP00000346827:E347D	E	-	3	2	ALDH9A1	163905201	0.998000	0.40836	0.998000	0.56505	0.890000	0.51754	0.281000	0.18810	0.252000	0.21531	-0.446000	0.05623	GAA	.	.	none		0.438	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
MYO6	4646	hgsc.bcm.edu	37	6	76572352	76572352	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:76572352T>G	ENST00000369977.3	+	16	1725	c.1586T>G	c.(1585-1587)tTg>tGg	p.L529W	MYO6_ENST00000369981.3_Missense_Mutation_p.L529W|RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369985.4_Missense_Mutation_p.L529W|MYO6_ENST00000369975.1_Missense_Mutation_p.L529W	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	529	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CTGGATATTTTGGATGAAGAA	0.348																																					p.L529W		Atlas-SNP	.											.	MYO6	124	.	0			c.T1586G						PASS	.						103.0	94.0	97.0					6																	76572352		2203	4300	6503	SO:0001583	missense	4646	exon16			ATATTTTGGATGA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1586T>G	6.37:g.76572352T>G	ENSP00000358994:p.Leu529Trp	133.0	0.0	0		124.0	6.0	0.0483871	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123528	0.77436	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07	5.9	3.46	0.39613	.	0.000000	0.64402	D	0.000001	D	0.94820	0.8327	H	0.99719	4.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94846	0.8009	10	0.87932	D	0	.	11.41	0.49921	0.2412:0.0:0.0:0.7588	.	529;529	Q9UM54-2;Q9UM54-1	.;.	W	529	ENSP00000358998:L529W;ENSP00000359002:L529W;ENSP00000358994:L529W;ENSP00000358992:L529W	ENSP00000358992:L529W	L	+	2	0	MYO6	76629072	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	0.458000	0.26988	0.528000	0.53228	TTG	.	.	none		0.348	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
P2RY8	286530	hgsc.bcm.edu	37	X	1585084	1585084	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:1585084A>C	ENST00000381297.4	-	2	578	c.368T>G	c.(367-369)cTg>cGg	p.L123R	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CAGGACCCCCAGGAAGCGCTC	0.632			T	CRLF2	"""B-ALL, Downs associated ALL"""																																p.L123R		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.T368G						PASS	.						88.0	85.0	86.0					X																	1585084		2202	4296	6498	SO:0001583	missense	286530	exon2			ACCCCCAGGAAGC	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.368T>G	X.37:g.1585084A>C	ENSP00000370697:p.Leu123Arg	120.0	0.0	0		87.0	15.0	0.172414	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	a	14.57	2.573664	0.45902	.	.	ENSG00000182162	ENST00000381297	T	0.46819	0.86	2.26	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.242138	0.29300	U	0.012559	T	0.65428	0.2690	M	0.80028	2.48	0.09310	N	1	D	0.69078	0.997	D	0.70487	0.969	T	0.56836	-0.7913	10	0.72032	D	0.01	.	9.9318	0.41528	1.0:0.0:0.0:0.0	.	123	Q86VZ1	P2RY8_HUMAN	R	123	ENSP00000370697:L123R	ENSP00000370697:L123R	L	-	2	0	P2RY8	1545084	1.000000	0.71417	0.995000	0.50966	0.350000	0.29205	7.120000	0.77153	0.611000	0.30052	0.230000	0.17803	CTG	.	.	none		0.632	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
FAM135B	51059	hgsc.bcm.edu	37	8	139160926	139160926	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139160926A>G	ENST00000395297.1	-	14	3455	c.3285T>C	c.(3283-3285)ttT>ttC	p.F1095F		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1095										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGGCCTGATAAAAACTGGAGA	0.388										HNSCC(54;0.14)																											p.F1095F		Atlas-SNP	.											.	FAM135B	423	.	0			c.T3285C						PASS	.						30.0	30.0	30.0					8																	139160926		2203	4300	6503	SO:0001819	synonymous_variant	51059	exon14			CTGATAAAAACTG	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3285T>C	8.37:g.139160926A>G		41.0	0.0	0		49.0	13.0	0.265306	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			.	.	none		0.388	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840732	1840732	+	Silent	SNP	G	G	A	rs372962204		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1840732G>A	ENST00000331238.6	-	2	863	c.384C>T	c.(382-384)caC>caT	p.H128H		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GGTAGAGGGCGTGAAGCTTCA	0.657																																					p.H128H	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.C384T						PASS	.	G		2,4392		0,2,2195	49.0	55.0	53.0		384	-4.3	0.9	17		53	0,8582		0,0,4291	no	coding-synonymous	RTN4RL1	NM_178568.2		0,2,6486	AA,AG,GG		0.0,0.0455,0.0154		128/442	1840732	2,12974	2197	4291	6488	SO:0001819	synonymous_variant	146760	exon2			GAGGGCGTGAAGC	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"""nogo-66 receptor homolog 2"""	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.384C>T	17.37:g.1840732G>A		66.0	0.0	0		76.0	38.0	0.5	NM_178568		Silent	SNP	ENST00000331238.6	37	CCDS45569.1																																																																																			.	.	weak		0.657	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
MAP1B	4131	hgsc.bcm.edu	37	5	71491950	71491950	+	Missense_Mutation	SNP	T	T	C	rs143194383	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71491950T>C	ENST00000296755.7	+	5	3066	c.2768T>C	c.(2767-2769)aTt>aCt	p.I923T		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	923					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GTAGACGACATTGAAAAATTT	0.512													T|||	2	0.000399361	0.0	0.0014	5008	,	,		20663	0.0		0.001	False		,,,				2504	0.0				p.I923T	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T2768C						PASS	.	T	THR/ILE	5,4401	9.9+/-24.2	0,5,2198	56.0	62.0	60.0		2768	-5.8	0.0	5	dbSNP_134	60	14,8586	10.5+/-38.8	0,14,4286	yes	missense	MAP1B	NM_005909.3	89	0,19,6484	CC,CT,TT		0.1628,0.1135,0.1461	benign	923/2469	71491950	19,12987	2203	4300	6503	SO:0001583	missense	4131	exon5			ACGACATTGAAAA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2768T>C	5.37:g.71491950T>C	ENSP00000296755:p.Ile923Thr	74.0	0.0	0		83.0	49.0	0.590361	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	0.011	-1.725172	0.00694	0.001135	0.001628	ENSG00000131711	ENST00000296755	T	0.03004	4.08	5.6	-5.81	0.02340	.	0.728470	0.12932	N	0.427289	T	0.02012	0.0063	N	0.22421	0.69	0.20489	N	0.999891	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47959	-0.9076	10	0.12430	T	0.62	-0.4578	8.5315	0.33337	0.1813:0.4869:0.0:0.3318	.	797;923	A2BDK6;P46821	.;MAP1B_HUMAN	T	923	ENSP00000296755:I923T	ENSP00000296755:I923T	I	+	2	0	MAP1B	71527706	0.055000	0.20627	0.010000	0.14722	0.054000	0.15201	-0.302000	0.08221	-0.724000	0.04908	-0.353000	0.07706	ATT	T|1.000;C|0.000	0.000	strong		0.512	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
KCNJ2	3759	hgsc.bcm.edu	37	17	68171425	68171425	+	Missense_Mutation	SNP	G	G	A	rs199473653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:68171425G>A	ENST00000243457.3	+	2	628	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	KCNJ2_ENST00000535240.1_Missense_Mutation_p.R82Q	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	82					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					ATTCGCTGGCGGTGGATGCTG	0.512																																					p.R82Q		Atlas-SNP	.											.	KCNJ2	74	.	0			c.G245A	GRCh37	CM053932	KCNJ2	M		PASS	.						220.0	164.0	183.0					17																	68171425		2203	4300	6503	SO:0001583	missense	3759	exon2			GCTGGCGGTGGAT	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.245G>A	17.37:g.68171425G>A	ENSP00000243457:p.Arg82Gln	285.0	0.0	0		306.0	85.0	0.277778	NM_000891	O15110|P48049	Missense_Mutation	SNP	ENST00000243457.3	37	CCDS11688.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689148	0.88735	.	.	ENSG00000123700	ENST00000535240;ENST00000243457	D;D	0.95788	-3.81;-3.81	5.66	5.66	0.87406	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98692	0.9561	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99379	1.0922	9	.	.	.	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	82	P63252	IRK2_HUMAN	Q	82	ENSP00000441848:R82Q;ENSP00000243457:R82Q	.	R	+	2	0	KCNJ2	65683020	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.662000	0.90505	0.555000	0.69702	CGG	.	.	weak		0.512	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
ENTPD1	953	hgsc.bcm.edu	37	10	97471746	97471746	+	Silent	SNP	G	G	A	rs200247284	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:97471746G>A	ENST00000453258.2	+	1	211	c.33G>A	c.(31-33)caG>caA	p.Q11Q		NM_001098175.1	NP_001091645.1	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	0					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		caagccagcagaagggtaaga	0.498													G|||	6	0.00119808	0.0	0.0	5008	,	,		17840	0.0		0.006	False		,,,				2504	0.0				p.Q11Q		Atlas-SNP	.											.	ENTPD1	44	.	0			c.G33A						PASS	.	G		2,3754		0,2,1876	59.0	65.0	63.0		33	0.5	0.6	10		63	40,8154		0,40,4057	no	coding-synonymous	ENTPD1	NM_001098175.1		0,42,5933	AA,AG,GG		0.4882,0.0532,0.3515		11/518	97471746	42,11908	1878	4097	5975	SO:0001819	synonymous_variant	953	exon1			CCAGCAGAAGGGT	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000453258.2:c.33G>A	10.37:g.97471746G>A		64.0	0.0	0		76.0	33.0	0.434211	NM_001098175	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Silent	SNP	ENST00000453258.2	37	CCDS41554.1																																																																																			G|0.994;A|0.006	0.006	strong		0.498	ENTPD1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049563.1	NM_001776	
NBR1	4077	hgsc.bcm.edu	37	17	41342737	41342737	+	Silent	SNP	G	G	A	rs200554551	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:41342737G>A	ENST00000422280.1	+	9	1266	c.807G>A	c.(805-807)ccG>ccA	p.P269P	NBR1_ENST00000341165.6_Silent_p.P269P|NBR1_ENST00000590996.1_Silent_p.P269P|NBR1_ENST00000589872.1_Silent_p.P269P|NBR1_ENST00000542611.1_Silent_p.P248P|NBR1_ENST00000389312.4_Silent_p.P269P	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	269					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		CCTCTGAACCGTTCTGTCACT	0.483													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18864	0.0		0.003	False		,,,				2504	0.0				p.P269P		Atlas-SNP	.											.	NBR1	55	.	0			c.G807A						PASS	.	G	,,	5,3885		0,5,1940	141.0	135.0	137.0		807,807,807	-11.9	0.0	17		137	53,8223		0,53,4085	no	coding-synonymous,coding-synonymous,coding-synonymous	NBR1	NM_005899.3,NM_031858.2,NM_031862.2	,,	0,58,6025	AA,AG,GG		0.6404,0.1285,0.4767	,,	269/967,269/967,269/967	41342737	58,12108	1945	4138	6083	SO:0001819	synonymous_variant	4077	exon9			TGAACCGTTCTGT	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"""membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"""	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.807G>A	17.37:g.41342737G>A		124.0	0.0	0		107.0	48.0	0.448598	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Silent	SNP	ENST00000422280.1	37	CCDS45694.1																																																																																			G|0.997;A|0.003	0.003	strong		0.483	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899	
ALK	238	hgsc.bcm.edu	37	2	29543736	29543736	+	Missense_Mutation	SNP	A	A	G	rs35093491	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29543736A>G	ENST00000389048.3	-	7	2333	c.1427T>C	c.(1426-1428)gTg>gCg	p.V476A	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	476			V -> A (in dbSNP:rs35093491). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GTAAAAACCCACAGGCAGTTT	0.512			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				A|||	80	0.0159744	0.0008	0.0216	5008	,	,		20583	0.0		0.0427	False		,,,				2504	0.0215				p.V476A		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.T1427C						PASS	.	A	ALA/VAL	30,4376	35.2+/-66.4	0,30,2173	165.0	152.0	156.0		1427	3.0	0.9	2	dbSNP_126	156	326,8274	114.6+/-174.5	4,318,3978	yes	missense	ALK	NM_004304.4	64	4,348,6151	GG,GA,AA		3.7907,0.6809,2.7372	benign	476/1621	29543736	356,12650	2203	4300	6503	SO:0001583	missense	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AAACCCACAGGCA	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1427T>C	2.37:g.29543736A>G	ENSP00000373700:p.Val476Ala	80.0	0.0	0		97.0	48.0	0.494845	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	35	0.016025641025641024	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	28	0.036939313984168866	A	1.964	-0.438159	0.04636	0.006809	0.037907	ENSG00000171094	ENST00000389048	T	0.01933	4.55	5.87	2.96	0.34315	Concanavalin A-like lectin/glucanase (1);	0.461885	0.18118	N	0.151131	T	0.00356	0.0011	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57573	-0.7788	9	.	.	.	.	6.3805	0.21531	0.1514:0.0:0.7015:0.1471	rs35093491;rs61744478	476	Q9UM73	ALK_HUMAN	A	476	ENSP00000373700:V476A	.	V	-	2	0	ALK	29397240	0.990000	0.36364	0.947000	0.38551	0.008000	0.06430	0.866000	0.27954	0.451000	0.26802	-0.177000	0.13119	GTG	A|0.973;G|0.027	0.027	strong		0.512	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
ACOT4	122970	hgsc.bcm.edu	37	14	74061757	74061757	+	Missense_Mutation	SNP	A	A	G	rs141714008		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74061757A>G	ENST00000326303.4	+	3	919	c.665A>G	c.(664-666)aAa>aGa	p.K222R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	222					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TTCCAGGTAAAAGGCCCAGGC	0.478																																					p.K222R		Atlas-SNP	.											.	ACOT4	25	.	0			c.A665G						PASS	.	A	ARG/LYS	0,4406		0,0,2203	93.0	102.0	99.0		665	5.4	1.0	14	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACOT4	NM_152331.3	26	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	222/422	74061757	1,13005	2203	4300	6503	SO:0001583	missense	122970	exon3			AGGTAAAAGGCCC	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.665A>G	14.37:g.74061757A>G	ENSP00000323071:p.Lys222Arg	153.0	0.0	0		122.0	59.0	0.483607	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.326631	0.41197	0.0	1.16E-4	ENSG00000177465	ENST00000326303	T	0.42131	0.98	5.41	5.41	0.78517	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.155471	0.56097	D	0.000021	T	0.37073	0.0990	L	0.38838	1.175	0.80722	D	1	B	0.24043	0.096	B	0.33750	0.169	T	0.21621	-1.0240	10	0.39692	T	0.17	-13.6392	11.1594	0.48507	0.8459:0.1541:0.0:0.0	.	222	Q8N9L9	ACOT4_HUMAN	R	222	ENSP00000323071:K222R	ENSP00000323071:K222R	K	+	2	0	ACOT4	73131510	0.449000	0.25689	0.993000	0.49108	0.954000	0.61252	2.093000	0.41710	2.051000	0.60960	0.459000	0.35465	AAA	A|1.000;G|0.000	0.000	weak		0.478	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
NELL1	4745	hgsc.bcm.edu	37	11	20939776	20939776	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20939776A>T	ENST00000357134.5	+	6	804	c.652A>T	c.(652-654)Aca>Tca	p.T218S	NELL1_ENST00000298925.5_Missense_Mutation_p.T246S|NELL1_ENST00000325319.5_Missense_Mutation_p.T161S|NELL1_ENST00000532434.1_Missense_Mutation_p.T218S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	218	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TGGATATATAACACAGTGTCC	0.353																																					p.T218S		Atlas-SNP	.											.	NELL1	179	.	0			c.A652T						PASS	.						155.0	148.0	150.0					11																	20939776		2203	4299	6502	SO:0001583	missense	4745	exon6			TATATAACACAGT	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.652A>T	11.37:g.20939776A>T	ENSP00000349654:p.Thr218Ser	90.0	0.0	0		96.0	20.0	0.208333	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.606104	0.46527	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78924	-1.22;-1.19;-1.06;-1.1	5.93	4.81	0.61882	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.61553	0.2356	N	0.24115	0.695	0.38160	D	0.939013	B;B;B;B	0.31548	0.041;0.024;0.328;0.024	B;B;B;B	0.36186	0.029;0.013;0.219;0.007	T	0.56426	-0.7981	10	0.06757	T	0.87	-3.5175	8.232	0.31603	0.815:0.0:0.0656:0.1194	.	161;246;218;218	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	246;218;161;218	ENSP00000298925:T246S;ENSP00000349654:T218S;ENSP00000317837:T161S;ENSP00000437170:T218S	ENSP00000298925:T246S	T	+	1	0	NELL1	20896352	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.618000	0.61211	1.077000	0.40990	0.533000	0.62120	ACA	.	.	none		0.353	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
CACFD1	11094	hgsc.bcm.edu	37	9	136333487	136333487	+	Intron	SNP	G	G	A	rs3094381	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136333487G>A	ENST00000316948.4	+	5	508				CACFD1_ENST00000540581.1_Missense_Mutation_p.A152T|CACFD1_ENST00000542192.1_Missense_Mutation_p.A110T|CACFD1_ENST00000291722.7_Intron|SLC2A6_ENST00000485978.1_5'Flank	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1						synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										tggttccttcgcagcccagca	0.622													T|||	329	0.0656949	0.1188	0.0793	5008	,	,		17882	0.002		0.0974	False		,,,				2504	0.0174				p.A152T		Atlas-SNP	.											.	CACFD1	1	.	0			c.G454A						PASS	.																																			SO:0001627	intron_variant	11094	exon5			TCCTTCGCAGCCC		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"""chromosome 9 open reading frame 7"""	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.429-198G>A	9.37:g.136333487G>A		5.0	0.0	0		6.0	5.0	0.833333	NM_001242369	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Missense_Mutation	SNP	ENST00000316948.4	37	CCDS6974.1	171	0.0782967032967033	64	0.13008130081300814	33	0.09116022099447514	0	0.0	74	0.09762532981530343	T	16.65	3.183129	0.57800	.	.	ENSG00000160325	ENST00000540581;ENST00000542192	T;T	0.56611	0.45;0.48	3.01	-2.83	0.05769	.	.	.	.	.	T	0.00271	0.0008	L	0.38175	1.15	0.80722	P	0.0	B;P	0.43662	0.023;0.814	B;B	0.30572	0.001;0.117	T	0.04767	-1.0928	8	0.22706	T	0.39	.	1.0467	0.01571	0.3428:0.1156:0.338:0.2036	rs3094381;rs58053859;rs3094381	110;152	B7Z5E1;F5GXX4	.;.	T	152;110	ENSP00000440832:A152T;ENSP00000444328:A110T	ENSP00000440832:A152T	A	+	1	0	C9orf7	135323308	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.497000	0.00969	-0.693000	0.05121	-0.494000	0.04653	GCA	G|0.912;A|0.088	0.088	strong		0.622	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586	
NOP9	161424	hgsc.bcm.edu	37	14	24772965	24772965	+	Silent	SNP	C	C	A	rs116960868	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24772965C>A	ENST00000267425.3	+	7	1405	c.1312C>A	c.(1312-1314)Cgg>Agg	p.R438R	NOP9_ENST00000396802.3_Silent_p.R438R	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	438							poly(A) RNA binding (GO:0044822)										GCCCTCATCCCGGCAAGTGGC	0.527													C|||	26	0.00519169	0.0	0.0101	5008	,	,		20648	0.0		0.0189	False		,,,				2504	0.0				p.R438R		Atlas-SNP	.											C14orf21,colon,carcinoma,-2,1	.	.	1	0			c.C1312A						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	78.0	73.0	75.0		1312	4.4	1.0	14	dbSNP_132	75	125,8475	64.6+/-126.8	0,125,4175	no	coding-synonymous	C14orf21	NM_174913.1		0,139,6364	AA,AC,CC		1.4535,0.3177,1.0687		438/637	24772965	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon7			TCATCCCGGCAAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1312C>A	14.37:g.24772965C>A		112.0	0.0	0		111.0	56.0	0.504505	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			C|0.990;A|0.010	0.010	strong		0.527	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
RSPH6A	81492	hgsc.bcm.edu	37	19	46313918	46313918	+	Silent	SNP	C	C	G	rs141102105		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46313918C>G	ENST00000221538.3	-	2	973	c.831G>C	c.(829-831)gcG>gcC	p.A277A	RSPH6A_ENST00000597055.1_Silent_p.A277A|RSPH6A_ENST00000600188.1_Silent_p.A13A	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	277						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GGGTGAACAGCGCCTTCTGTT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17889	0.0		0.001	False		,,,				2504	0.0				p.A277A		Atlas-SNP	.											RSPH6A,NS,carcinoma,-2,1	RSPH6A	70	1	0			c.G831C						PASS	.	C		4,4402	9.9+/-24.2	0,4,2199	143.0	127.0	133.0		831	-3.8	1.0	19	dbSNP_134	133	44,8556	27.9+/-77.7	0,44,4256	no	coding-synonymous	RSPH6A	NM_030785.3		0,48,6455	GG,GC,CC		0.5116,0.0908,0.3691		277/718	46313918	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	81492	exon2			GAACAGCGCCTTC	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.831G>C	19.37:g.46313918C>G		93.0	0.0	0		64.0	33.0	0.515625	NM_030785	Q53FE2|Q6PEZ9	Silent	SNP	ENST00000221538.3	37	CCDS12675.1																																																																																			C|0.997;G|0.003	0.003	strong		0.637	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
LMX1A	4009	hgsc.bcm.edu	37	1	165322487	165322487	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165322487C>A	ENST00000342310.3	-	3	471	c.89G>T	c.(88-90)aGc>aTc	p.S30I	LMX1A_ENST00000294816.2_Missense_Mutation_p.S30I|LMX1A_ENST00000367893.4_Missense_Mutation_p.S30I	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	30					axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					AGACTTGGGGCTCACCGCTCT	0.637																																					p.S30I		Atlas-SNP	.											.	LMX1A	87	.	0			c.G89T						PASS	.						30.0	30.0	30.0					1																	165322487		2203	4299	6502	SO:0001583	missense	4009	exon3			TTGGGGCTCACCG	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"""Homeoboxes / LIM class"""	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.89G>T	1.37:g.165322487C>A	ENSP00000340226:p.Ser30Ile	36.0	0.0	0		38.0	11.0	0.289474	NM_001174069	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Missense_Mutation	SNP	ENST00000342310.3	37	CCDS1247.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192981	0.38707	.	.	ENSG00000162761	ENST00000342310;ENST00000294816;ENST00000367893	D;D;D	0.87029	-2.2;-2.2;-2.2	5.56	4.55	0.56014	.	0.485820	0.24426	N	0.038640	T	0.58163	0.2103	N	0.08118	0	0.28227	N	0.92627	B	0.10296	0.003	B	0.04013	0.001	T	0.53464	-0.8435	9	0.40728	T	0.16	.	6.8856	0.24197	0.0:0.6971:0.1832:0.1197	.	30	Q8TE12	LMX1A_HUMAN	I	30	ENSP00000340226:S30I;ENSP00000294816:S30I;ENSP00000356868:S30I	ENSP00000294816:S30I	S	-	2	0	LMX1A	163589111	0.989000	0.36119	1.000000	0.80357	0.995000	0.86356	0.505000	0.22642	2.606000	0.88127	0.561000	0.74099	AGC	.	.	none		0.637	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398	
TFEC	22797	hgsc.bcm.edu	37	7	115580893	115580893	+	Silent	SNP	G	G	A	rs34298819	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:115580893G>A	ENST00000265440.7	-	8	936	c.756C>T	c.(754-756)agC>agT	p.S252S	TFEC_ENST00000320239.7_Silent_p.S223S|TFEC_ENST00000393485.1_3'UTR|TFEC_ENST00000457268.1_Silent_p.S185S	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	252					cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			GCTCAGGATGGCTCTGCTGTT	0.483													G|||	26	0.00519169	0.0015	0.0086	5008	,	,		18076	0.0		0.0179	False		,,,				2504	0.0				p.S252S		Atlas-SNP	.											.	TFEC	51	.	0			c.C756T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	139.0	139.0	139.0		669,756	-1.6	0.9	7	dbSNP_126	139	134,8466	66.3+/-128.7	2,130,4168	no	coding-synonymous,coding-synonymous	TFEC	NM_001018058.2,NM_012252.3	,	2,144,6357	AA,AG,GG		1.5581,0.3177,1.1379	,	223/319,252/348	115580893	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	22797	exon8			AGGATGGCTCTGC	D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"""Basic helix-loop-helix proteins"""	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.756C>T	7.37:g.115580893G>A		153.0	0.0	0		147.0	70.0	0.47619	NM_012252	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Silent	SNP	ENST00000265440.7	37	CCDS5762.1																																																																																			G|0.988;A|0.012	0.012	strong		0.483	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252	
PEG3	5178	hgsc.bcm.edu	37	19	57335959	57335959	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57335959T>C	ENST00000326441.9	-	4	428	c.65A>G	c.(64-66)gAg>gGg	p.E22G	ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.E22G|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Intron|PEG3_ENST00000598410.1_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000594706.1_Intron|ZIM2_ENST00000593931.1_5'Flank	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	22					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ACTGTCTAGCTCATACAGATT	0.448																																					p.E22G		Atlas-SNP	.											.	PEG3	414	.	0			c.A65G						PASS	.						64.0	70.0	68.0					19																	57335959		2203	4300	6503	SO:0001583	missense	5178	exon3			TCTAGCTCATACA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.65A>G	19.37:g.57335959T>C	ENSP00000326581:p.Glu22Gly	140.0	0.0	0		135.0	35.0	0.259259	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555636	0.65425	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02944	4.1;4.1	4.66	2.49	0.30216	.	0.391735	0.18780	N	0.131365	T	0.01905	0.0060	N	0.24115	0.695	.	.	.	B	0.26363	0.147	B	0.18263	0.021	T	0.38950	-0.9637	8	.	.	.	-15.7338	5.0558	0.14531	0.0:0.0988:0.184:0.7172	.	22	Q9GZU2	PEG3_HUMAN	G	22	ENSP00000326581:E22G;ENSP00000403051:E22G	.	E	-	2	0	ZIM2	62027771	0.587000	0.26791	0.856000	0.33681	0.999000	0.98932	0.664000	0.25068	0.340000	0.23745	0.533000	0.62120	GAG	.	.	none		0.448	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
HIST2H2AC	8338	hgsc.bcm.edu	37	1	149858806	149858806	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149858806G>A	ENST00000331380.2	+	1	282	c.282G>A	c.(280-282)ctG>ctA	p.L94L	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	94						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L94L(2)		NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACGAGGAACTGAACAAGCTGC	0.582																																					p.L94L		Atlas-SNP	.											HIST2H2AC,NS,carcinoma,0,3	HIST2H2AC	75	3	2	Substitution - coding silent(2)	lung(2)	c.G282A						PASS	.						71.0	71.0	71.0					1																	149858806		2203	4298	6501	SO:0001819	synonymous_variant	8338	exon1			GGAACTGAACAAG	AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"""Histones / Replication-dependent"""	4738	protein-coding gene	gene with protein product		602797	"""H2A histone family, member Q"", ""histone 2, H2ac"""	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.282G>A	1.37:g.149858806G>A		211.0	0.0	0		209.0	11.0	0.0526316	NM_003517	Q6DRA7|Q8IUE5	Silent	SNP	ENST00000331380.2	37	CCDS937.1																																																																																			.	.	none		0.582	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517	
EDRF1	26098	hgsc.bcm.edu	37	10	127412393	127412393	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127412393T>C	ENST00000356792.4	+	4	630	c.398T>C	c.(397-399)cTc>cCc	p.L133P	C10orf137_ENST00000337623.3_Missense_Mutation_p.L133P	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ATAAAAAAACTCCTGAAAATT	0.323																																					p.L133P		Atlas-SNP	.											.	C10orf137	153	.	0			c.T398C						PASS	.						74.0	84.0	80.0					10																	127412393		2203	4299	6502	SO:0001583	missense	26098	exon4			AAAAACTCCTGAA																												ENST00000356792.4:c.398T>C	10.37:g.127412393T>C	ENSP00000349244:p.Leu133Pro	113.0	0.0	0		102.0	17.0	0.166667	NM_015608	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347429	0.82022	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	.	.	.	5.72	5.72	0.89469	.	0.128515	0.53938	D	0.000045	T	0.78084	0.4228	M	0.72479	2.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.80638	-0.1293	9	0.87932	D	0	.	14.5722	0.68218	0.0:0.0:0.0:1.0	.	133;133;133	Q3B7T1;Q3B7T1-5;Q3B7T1-3	EDRF1_HUMAN;.;.	P	133	.	ENSP00000336727:L133P	L	+	2	0	C10orf137	127402383	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.177000	0.69029	0.528000	0.53228	CTC	.	.	none		0.323	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1		
NT5C1B	93034	hgsc.bcm.edu	37	2	18767638	18767638	+	Missense_Mutation	SNP	A	A	G	rs147855918	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:18767638A>G	ENST00000359846.2	-	4	397	c.320T>C	c.(319-321)cTg>cCg	p.L107P	NT5C1B_ENST00000460052.1_5'UTR|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.L107P|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000304081.4_Missense_Mutation_p.L47P|NT5C1B_ENST00000600945.1_Missense_Mutation_p.L107P	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	107	Ser-rich.				nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TGTCTTCCGCAGTGATGATTC	0.498													a|||	10	0.00199681	0.0008	0.0086	5008	,	,		19665	0.0		0.003	False		,,,				2504	0.0				p.L124P		Atlas-SNP	.											.	NT5C1B	72	.	0			c.T371C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	6,4400	11.4+/-27.6	0,6,2197	109.0	96.0	100.0		320,269,371,320,140,320,140	1.9	0.0	2	dbSNP_134	100	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense,missense,missense,missense,missense,missense	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	98,98,98,98,98,98,98	0,60,6443	GG,GA,AA		0.6279,0.1362,0.4613	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	107/611,90/594,124/628,107/613,47/651,107/603,47/551	18767638	60,12946	2203	4300	6503	SO:0001583	missense	93034	exon4			TTCCGCAGTGATG	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.320T>C	2.37:g.18767638A>G	ENSP00000352904:p.Leu107Pro	113.0	0.0	0		130.0	59.0	0.453846	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	7	0.003205128205128205	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	2	0.002638522427440633	a	8.645	0.896775	0.17686	0.001362	0.006279	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846;ENST00000416783	D	0.91631	-2.88	4.23	1.86	0.25419	.	2.009920	0.02795	N	0.122481	D	0.86952	0.6057	L	0.27053	0.805	0.09310	N	0.999997	B;B;P;B;P;P;P;P	0.52692	0.001;0.0;0.828;0.001;0.736;0.892;0.924;0.955	B;B;B;B;B;P;B;P	0.50537	0.0;0.0;0.44;0.002;0.282;0.643;0.44;0.643	T	0.78656	-0.2119	10	0.49607	T	0.09	-11.0741	5.9108	0.19027	0.7916:0.0:0.2084:0.0	.	90;124;47;90;47;47;107;107	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;5NT1B_HUMAN;.	P	107;47;47;107;124	ENSP00000412639:L47P	ENSP00000305979:L47P	L	-	2	0	NT5C1B-RDH14;NT5C1B	18631119	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.628000	0.24522	0.431000	0.26258	-0.253000	0.11424	CTG	A|0.997;G|0.003	0.003	strong		0.498	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
ZEB2	9839	hgsc.bcm.edu	37	2	145274844	145274844	+	Splice_Site	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:145274844C>T	ENST00000558170.2	-	2	1258		c.e2+1		ZEB2-AS1_ENST00000421083.1_RNA|ZEB2-AS1_ENST00000602006.1_RNA|ZEB2-AS1_ENST00000609376.1_RNA|ZEB2-AS1_ENST00000595109.1_RNA|ZEB2_ENST00000465070.1_Splice_Site|ZEB2_ENST00000493689.1_Splice_Site|ZEB2-AS1_ENST00000609842.1_RNA|ZEB2-AS1_ENST00000427278.3_RNA|ZEB2_ENST00000462355.1_Splice_Site|ZEB2-AS1_ENST00000609819.1_RNA|ZEB2_ENST00000539609.3_Splice_Site|ZEB2-AS1_ENST00000610265.1_RNA|ZEB2_ENST00000303660.4_Splice_Site|ZEB2-AS1_ENST00000608361.1_RNA|ZEB2_ENST00000470879.1_Splice_Site|ZEB2_ENST00000409487.3_Splice_Site|ZEB2-AS1_ENST00000428623.1_RNA	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2						cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CTGCTTCTTACCGTTTTTCCT	0.602																																					.	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,NS,0,1	ZEB2	218	1	0			c.73+1G>A	GRCh37	CS031468	ZEB2	S		PASS	.						175.0	182.0	180.0					2																	145274844		2203	4300	6503	SO:0001630	splice_region_variant	9839	exon3			TTCTTACCGTTTT	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.73+1G>A	2.37:g.145274844C>T		56.0	0.0	0		50.0	27.0	0.54	NM_001171653	A0JP09|B7Z2P2|F5H814|Q9UED1	Splice_Site	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140744	0.56936	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861;ENST00000431672;ENST00000409211;ENST00000435831;ENST00000444559	.	.	.	3.3	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7876	0.46413	0.2422:0.7578:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZEB2	144991314	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.742000	0.74843	1.789000	0.52484	0.442000	0.29010	.	.	.	none		0.602	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	Intron
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:67802190A>T	ENST00000377865.2	-	1	517	c.383T>A	c.(382-384)aTa>aAa	p.I128K	PCDH9_ENST00000328454.5_Missense_Mutation_p.I128K|PCDH9_ENST00000456367.1_Missense_Mutation_p.I128K|PCDH9_ENST00000544246.1_Missense_Mutation_p.I128K|PCDH9_ENST00000377861.3_Missense_Mutation_p.I128K			Q9HC56	PCDH9_HUMAN	protocadherin 9	128	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AATTATTTTTATTTTGATCAG	0.408																																					p.I128K		Atlas-SNP	.											.	PCDH9	252	.	0			c.T383A						PASS	.						87.0	89.0	88.0					13																	67802190		2203	4300	6503	SO:0001583	missense	5101	exon2			ATTTTTATTTTGA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.383T>A	13.37:g.67802190A>T	ENSP00000367096:p.Ile128Lys	103.0	0.0	0		154.0	54.0	0.350649	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.975540	0.53720	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.58797	0.37;0.37;0.31;0.31;0.32	5.94	5.94	0.96194	Cadherin (3);	0.000000	0.85682	D	0.000000	T	0.81781	0.4895	M	0.92784	3.345	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.78314	0.961;0.979;0.991;0.979	D	0.86032	0.1514	10	0.66056	D	0.02	.	16.3947	0.83586	1.0:0.0:0.0:0.0	.	128;128;128;128	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	K	128	ENSP00000442186:I128K;ENSP00000367096:I128K;ENSP00000401699:I128K;ENSP00000332060:I128K;ENSP00000367092:I128K	ENSP00000332060:I128K	I	-	2	0	PCDH9	66700191	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.272000	0.75746	0.459000	0.35465	ATA	.	.	none		0.408	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
NUP62	23636	hgsc.bcm.edu	37	19	50412396	50412396	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50412396C>T	ENST00000596217.1	-	2	2556	c.669G>A	c.(667-669)gcG>gcA	p.A223A	NUP62_ENST00000597029.1_Silent_p.A223A|NUP62_ENST00000413454.1_Silent_p.A223A|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000352066.3_Silent_p.A223A|NUP62_ENST00000422090.2_Silent_p.A223A|IL4I1_ENST00000341114.3_Intron|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Silent_p.A223A			P37198	NUP62_HUMAN	nucleoporin 62kDa	223	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TTGCTATTGACGCAAAGAGGC	0.642																																					p.A223A		Atlas-SNP	.											NUP62,NS,carcinoma,0,2	NUP62	50	2	0			c.G669A						PASS	.						94.0	87.0	89.0					19																	50412396		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			TATTGACGCAAAG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.669G>A	19.37:g.50412396C>T		66.0	0.0	0		85.0	39.0	0.458824	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			.	.	none		0.642	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
GRIN2A	2903	hgsc.bcm.edu	37	16	9857231	9857231	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:9857231C>T	ENST00000396573.2	-	14	4479	c.4170G>A	c.(4168-4170)tcG>tcA	p.S1390S	GRIN2A_ENST00000330684.3_Silent_p.S1390S|GRIN2A_ENST00000396575.2_Silent_p.S1390S|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R1276H|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R1119H|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R1276H	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1390					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GGGATGGCAACGAGTGTTTGT	0.547																																					p.R1276H		Atlas-SNP	.											GRIN2A,colon,carcinoma,0,1	GRIN2A	366	1	0			c.G3827A						PASS	.						118.0	104.0	108.0					16																	9857231		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon14			TGGCAACGAGTGT		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.4170G>A	16.37:g.9857231C>T		99.0	0.0	0		86.0	32.0	0.372093	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.796460	0.31777	.	.	ENSG00000183454	ENST00000404927;ENST00000535259	T;T	0.12039	2.72;2.72	5.91	-6.96	0.01622	.	.	.	.	.	T	0.05273	0.0140	.	.	.	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.41805	-0.9488	7	.	.	.	.	4.2924	0.10885	0.0844:0.1963:0.4074:0.312	.	1119;1276	F5GZ52;Q17RZ6	.;.	H	1276;1119	ENSP00000385872:R1276H;ENSP00000441572:R1119H	.	R	-	2	0	GRIN2A	9764732	0.001000	0.12720	0.019000	0.16419	0.954000	0.61252	-0.160000	0.10041	-0.751000	0.04734	0.655000	0.94253	CGT	.	.	none		0.547	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
IGSF10	285313	hgsc.bcm.edu	37	3	151165641	151165641	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151165641T>G	ENST00000282466.3	-	4	2127	c.2128A>C	c.(2128-2130)Aaa>Caa	p.K710Q		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	710					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GAGGTGTGTTTTCCAACCTCA	0.488																																					p.K710Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A2128C						PASS	.						80.0	67.0	71.0					3																	151165641		2203	4300	6503	SO:0001583	missense	285313	exon4			TGTGTTTTCCAAC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.2128A>C	3.37:g.151165641T>G	ENSP00000282466:p.Lys710Gln	197.0	0.0	0		201.0	11.0	0.0547264	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.394224	0.25205	.	.	ENSG00000152580	ENST00000282466	T	0.69040	-0.37	4.66	4.66	0.58398	.	0.474372	0.17291	N	0.179644	T	0.50769	0.1635	L	0.29908	0.895	0.09310	N	1	B	0.21905	0.062	B	0.16289	0.015	T	0.31641	-0.9936	10	0.22109	T	0.4	.	9.5824	0.39495	0.0:0.0:0.2373:0.7627	.	710	Q6WRI0	IGS10_HUMAN	Q	710	ENSP00000282466:K710Q	ENSP00000282466:K710Q	K	-	1	0	IGSF10	152648331	0.002000	0.14202	0.024000	0.17045	0.020000	0.10135	0.929000	0.28844	1.876000	0.54355	0.482000	0.46254	AAA	.	.	none		0.488	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874241	31874241	+	Silent	SNP	G	G	T	rs150340950	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31874241G>T	ENST00000334151.2	-	1	194	c.168C>A	c.(166-168)cgC>cgA	p.R56R		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	56						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						GACGGCAGCTGCGGTATCCAT	0.527													G|||	28	0.00559105	0.0015	0.0072	5008	,	,		17028	0.0		0.0189	False		,,,				2504	0.002				p.R56R		Atlas-SNP	.											KRTAP19-5,NS,carcinoma,-2,1	KRTAP19-5	32	1	0			c.C168A						PASS	.						112.0	110.0	110.0					21																	31874241		2203	4300	6503	SO:0001819	synonymous_variant	337972	exon1			GCAGCTGCGGTAT	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"""Keratin associated proteins"""	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.168C>A	21.37:g.31874241G>T		57.0	0.0	0		66.0	23.0	0.348485	NM_181611	A4IF22	Silent	SNP	ENST00000334151.2	37	CCDS13597.1																																																																																			G|0.975;T|0.025	0.025	strong		0.527	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2		
POM121L2	94026	hgsc.bcm.edu	37	6	27278340	27278340	+	Missense_Mutation	SNP	A	A	G	rs147268352	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27278340A>G	ENST00000444565.1	-	1	1609	c.1610T>C	c.(1609-1611)aTt>aCt	p.I537T	POM121L2_ENST00000377451.2_Missense_Mutation_p.I473T	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	537										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						GGGCCCCAAAATCGGTTTTAA	0.468													A|||	2	0.000399361	0.0008	0.0014	5008	,	,		19877	0.0		0.0	False		,,,				2504	0.0				p.I537T		Atlas-SNP	.											.	POM121L2	61	.	0			c.T1610C						PASS	.						30.0	28.0	29.0					6																	27278340		692	1591	2283	SO:0001583	missense	94026	exon1			CCCAAAATCGGTT	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.1610T>C	6.37:g.27278340A>G	ENSP00000392726:p.Ile537Thr	79.0	0.0	0		110.0	24.0	0.218182	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	A	9.393	1.076084	0.20227	.	.	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.23950	1.88;2.09	4.2	-2.58	0.06228	.	2.365940	0.02141	N	0.057161	T	0.08891	0.0220	M	0.68317	2.08	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.20940	-1.0260	10	0.21014	T	0.42	.	4.4149	0.11452	0.3806:0.3331:0.2863:0.0	.	537	C9J1I7	.	T	473;537	ENSP00000366671:I473T;ENSP00000392726:I537T	ENSP00000366671:I473T	I	-	2	0	POM121L2	27386319	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.140000	0.16056	-0.446000	0.07149	-0.421000	0.06004	ATT	A|0.999;G|0.001	0.001	strong		0.468	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
CCDC15	80071	hgsc.bcm.edu	37	11	124857192	124857192	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124857192A>C	ENST00000344762.5	+	8	1329	c.1070A>C	c.(1069-1071)aAg>aCg	p.K357T	CCDC15_ENST00000529051.1_Missense_Mutation_p.K357T	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	357						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		CAGAGTGTTAAGCCAGATACC	0.493																																					p.K357T		Atlas-SNP	.											.	CCDC15	134	.	0			c.A1070C						PASS	.						124.0	119.0	121.0					11																	124857192		1838	4093	5931	SO:0001583	missense	80071	exon8			GTGTTAAGCCAGA	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.1070A>C	11.37:g.124857192A>C	ENSP00000341684:p.Lys357Thr	138.0	0.0	0		137.0	20.0	0.145985	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.721457	0.30503	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.32272	1.46;1.46	4.09	1.72	0.24424	.	1.268580	0.05276	N	0.518579	T	0.17280	0.0415	N	0.08118	0	0.09310	N	1	P	0.41848	0.763	B	0.39027	0.288	T	0.17868	-1.0355	10	0.72032	D	0.01	-0.6297	5.4022	0.16303	0.7249:0.1776:0.0975:0.0	.	357	Q0P6D6	CCD15_HUMAN	T	357	ENSP00000435403:K357T;ENSP00000341684:K357T	ENSP00000341684:K357T	K	+	2	0	CCDC15	124362402	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.049000	0.11924	0.369000	0.24510	0.379000	0.24179	AAG	.	.	none		0.493	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
FAIM3	9214	hgsc.bcm.edu	37	1	207078467	207078467	+	Missense_Mutation	SNP	G	G	A	rs41304091	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207078467G>A	ENST00000367091.3	-	8	1213	c.1070C>T	c.(1069-1071)gCc>gTc	p.A357V	FAIM3_ENST00000442471.2_Missense_Mutation_p.A245V|FAIM3_ENST00000420007.2_3'UTR|FAIM3_ENST00000528654.1_5'UTR	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	357					cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					CAGAGATGGGGCATGGAGCCA	0.502													G|||	8	0.00159744	0.0	0.0	5008	,	,		19983	0.0		0.008	False		,,,				2504	0.0				p.A357V		Atlas-SNP	.											.	FAIM3	36	.	0			c.C1070T						PASS	.	G	VAL/ALA,,VAL/ALA	16,4390	23.3+/-48.9	0,16,2187	114.0	108.0	110.0		734,,1070	2.0	0.0	1	dbSNP_127	110	128,8472	65.3+/-127.6	0,128,4172	yes	missense,utr-3,missense	FAIM3	NM_001142473.1,NM_001193338.1,NM_005449.4	64,,64	0,144,6359	AA,AG,GG		1.4884,0.3631,1.1072	benign,,benign	245/279,,357/391	207078467	144,12862	2203	4300	6503	SO:0001583	missense	9214	exon8			GATGGGGCATGGA	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.1070C>T	1.37:g.207078467G>A	ENSP00000356058:p.Ala357Val	65.0	0.0	0		64.0	23.0	0.359375	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Missense_Mutation	SNP	ENST00000367091.3	37	CCDS1473.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	2.553	-0.303557	0.05495	0.003631	0.014884	ENSG00000162894	ENST00000367091;ENST00000442471	T	0.24151	1.87	5.14	2.02	0.26589	.	0.514876	0.16940	N	0.193320	T	0.09598	0.0236	N	0.19112	0.55	0.09310	N	1	B;B;B	0.22746	0.074;0.074;0.044	B;B;B	0.20955	0.032;0.032;0.014	T	0.21280	-1.0250	10	0.34782	T	0.22	-5.9354	4.7727	0.13164	0.2118:0.1724:0.6158:0.0	rs41304091	266;245;357	B7Z497;B7Z6Z0;O60667	.;.;FAIM3_HUMAN	V	357;245	ENSP00000356058:A357V	ENSP00000356058:A357V	A	-	2	0	FAIM3	205145090	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.162000	0.16501	0.126000	0.18424	0.655000	0.94253	GCC	G|0.992;A|0.008	0.008	strong		0.502	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449	
SLC22A11	55867	hgsc.bcm.edu	37	11	64337280	64337280	+	Silent	SNP	G	G	A	rs34836439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64337280G>A	ENST00000301891.4	+	9	1913	c.1539G>A	c.(1537-1539)ccG>ccA	p.P513P	SLC22A11_ENST00000377585.3_Silent_p.P405P|SLC22A11_ENST00000377581.3_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	513					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	TCTTCCTCCCGGAGACCCAGG	0.622													G|||	11	0.00219649	0.0008	0.0144	5008	,	,		18022	0.0		0.0	False		,,,				2504	0.0				p.P513P		Atlas-SNP	.											.	SLC22A11	54	.	0			c.G1539A						PASS	.	G		1,4401	2.1+/-5.4	0,1,2200	113.0	105.0	108.0		1539	-7.1	0.1	11	dbSNP_126	108	4,8590	3.0+/-9.4	0,4,4293	no	coding-synonymous	SLC22A11	NM_018484.2		0,5,6493	AA,AG,GG		0.0465,0.0227,0.0385		513/551	64337280	5,12991	2201	4297	6498	SO:0001819	synonymous_variant	55867	exon9			CCTCCCGGAGACC	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.1539G>A	11.37:g.64337280G>A		38.0	0.0	0		44.0	20.0	0.454545	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	37	CCDS8074.1																																																																																			G|0.996;A|0.004	0.004	strong		0.622	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	
COL4A2	1284	hgsc.bcm.edu	37	13	111102770	111102770	+	Silent	SNP	C	C	T	rs78615289	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:111102770C>T	ENST00000360467.5	+	20	1614	c.1308C>T	c.(1306-1308)ccC>ccT	p.P436P		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	436	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CTCCAGGACCCCCCGGGCTCC	0.642													C|||	62	0.0123802	0.0461	0.0014	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.P436P		Atlas-SNP	.											.	COL4A2	178	.	0			c.C1308T						PASS	.	C		98,3596		1,96,1750	30.0	35.0	34.0		1308	-1.9	0.0	13	dbSNP_131	34	4,8174		0,4,4085	yes	coding-synonymous	COL4A2	NM_001846.2		1,100,5835	TT,TC,CC		0.0489,2.653,0.8592		436/1713	111102770	102,11770	1847	4089	5936	SO:0001819	synonymous_variant	1284	exon20			AGGACCCCCCGGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1308C>T	13.37:g.111102770C>T		28.0	0.0	0		18.0	8.0	0.444444	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
MRPS12	6183	hgsc.bcm.edu	37	19	39421979	39421979	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39421979T>G	ENST00000407800.2	+	1	386	c.45T>G	c.(43-45)acT>acG	p.T15T	MRPS12_ENST00000308018.4_Silent_p.T15T|SARS2_ENST00000221431.6_5'Flank|SARS2_ENST00000600042.1_5'Flank|SARS2_ENST00000430193.3_5'Flank|SARS2_ENST00000594171.1_5'Flank|CTC-360G5.8_ENST00000599996.1_Intron|MRPS12_ENST00000402029.3_Silent_p.T15T|SARS2_ENST00000448145.2_Intron	NM_021107.1	NP_066930.1	O15235	RT12_HUMAN	mitochondrial ribosomal protein S12	15					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(1)	2	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CGTCCCTAACTTGTGGTAAGT	0.592																																					p.T15T		Atlas-SNP	.											.	MRPS12	11	.	0			c.T45G						PASS	.						119.0	111.0	114.0					19																	39421979		2203	4300	6503	SO:0001819	synonymous_variant	6183	exon2			CCTAACTTGTGGT	Y11681	CCDS12525.1	19q13.1-q13.2	2012-09-13			ENSG00000128626	ENSG00000128626		"""Mitochondrial ribosomal proteins / small subunits"""	10380	protein-coding gene	gene with protein product		603021		RPMS12		9545647, 9790755	Standard	NM_021107		Approved	RPS12, RPSM12	uc002oke.3	O15235		ENST00000407800.2:c.45T>G	19.37:g.39421979T>G		84.0	0.0	0		94.0	27.0	0.287234	NM_033362	Q53X98	Silent	SNP	ENST00000407800.2	37	CCDS12525.1																																																																																			.	.	none		0.592	MRPS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463154.1		
WBSCR17	64409	hgsc.bcm.edu	37	7	71177023	71177023	+	Silent	SNP	G	G	A	rs75947590	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:71177023G>A	ENST00000333538.5	+	11	2323	c.1689G>A	c.(1687-1689)aaG>aaA	p.K563K	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	563	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TCATGAACAAGGGCACGGGAC	0.567													G|||	33	0.00658946	0.0	0.0231	5008	,	,		16311	0.006		0.0	False		,,,				2504	0.0112				p.K563K		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G1689A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	72.0	78.0	76.0		1689	-2.2	0.9	7	dbSNP_131	76	0,8600		0,0,4300	no	coding-synonymous	WBSCR17	NM_022479.1		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		563/599	71177023	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon11			GAACAAGGGCACG	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1689G>A	7.37:g.71177023G>A		57.0	0.0	0		58.0	28.0	0.482759	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
PRSS36	146547	hgsc.bcm.edu	37	16	31152818	31152818	+	Missense_Mutation	SNP	C	C	T	rs117442264	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31152818C>T	ENST00000268281.4	-	12	1931	c.1873G>A	c.(1873-1875)Gtc>Atc	p.V625I	PRSS36_ENST00000569305.1_Missense_Mutation_p.V620I|PRSS36_ENST00000418068.2_Missense_Mutation_p.V625I	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	625	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						GCTGCCAGGACCCAGCCTGGG	0.617													C|||	45	0.00898562	0.0023	0.0303	5008	,	,		15672	0.0		0.0199	False		,,,				2504	0.001				p.V625I		Atlas-SNP	.											.	PRSS36	50	.	0			c.G1873A						PASS	.	C	ILE/VAL	18,4376	23.3+/-48.9	0,18,2179	55.0	63.0	61.0		1873	4.3	1.0	16	dbSNP_132	61	130,8470	63.9+/-126.0	0,130,4170	yes	missense	PRSS36	NM_173502.3	29	0,148,6349	TT,TC,CC		1.5116,0.4096,1.139	probably-damaging	625/856	31152818	148,12846	2197	4300	6497	SO:0001583	missense	146547	exon12			CCAGGACCCAGCC	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.1873G>A	16.37:g.31152818C>T	ENSP00000268281:p.Val625Ile	25.0	0.0	0		32.0	12.0	0.375	NM_001258291	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	26	0.011904761904761904	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	12	0.0158311345646438	C	16.78	3.217405	0.58560	0.004096	0.015116	ENSG00000178226	ENST00000268281;ENST00000418068	T;D	0.87887	-0.48;-2.31	5.29	4.34	0.51931	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.64638	0.2616	L	0.49778	1.585	0.31588	N	0.654304	B;B;B	0.18310	0.027;0.025;0.025	B;B;B	0.20577	0.03;0.028;0.028	T	0.72786	-0.4188	9	0.33141	T	0.24	.	8.0067	0.30329	0.0:0.8159:0.0:0.1841	.	625;620;625	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	I	625	ENSP00000268281:V625I;ENSP00000407160:V625I	ENSP00000268281:V625I	V	-	1	0	PRSS36	31060319	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.299000	0.51826	1.226000	0.43582	0.455000	0.32223	GTC	C|0.990;T|0.010	0.010	strong		0.617	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
OGFR	11054	hgsc.bcm.edu	37	20	61444660	61444660	+	Missense_Mutation	SNP	C	C	A	rs61743079		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61444660C>A	ENST00000290291.6	+	7	1718	c.1693C>A	c.(1693-1695)Cgc>Agc	p.R565S	OGFR_ENST00000370461.1_Missense_Mutation_p.R513S	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	565	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCCAGGCCCCCGCCCGGCAGG	0.741																																					p.R565S		Atlas-SNP	.											OGFR,NS,neuroblastoma,0,1	OGFR	63	1	0			c.C1693A						scavenged	.						3.0	6.0	5.0					20																	61444660		1281	3014	4295	SO:0001583	missense	11054	exon7			GGCCCCCGCCCGG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1693C>A	20.37:g.61444660C>A	ENSP00000290291:p.Arg565Ser	4.0	0.0	0		8.0	3.0	0.375	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	A	0.130	-1.114132	0.01799	.	.	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.54866	0.55;0.55	1.46	-2.91	0.05631	.	.	.	.	.	T	0.23649	0.0572	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19031	-1.0318	9	0.11182	T	0.66	.	0.4172	0.00450	0.232:0.1649:0.1659:0.4372	rs61743079	565;548;565	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	S	565;545;400;513	ENSP00000290291:R565S;ENSP00000359491:R513S	ENSP00000290291:R565S	R	+	1	0	OGFR	60915105	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-0.466000	0.06672	-1.870000	0.01139	-1.293000	0.01348	CGC	C|0.981;A|0.019	0.019	weak		0.741	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
RAB21	23011	hgsc.bcm.edu	37	12	72148943	72148943	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:72148943G>A	ENST00000261263.3	+	1	290	c.34G>A	c.(34-36)Gcg>Acg	p.A12T		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	12					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)	6						cggcggggcggcggcggcggG	0.741																																					p.A12T		Atlas-SNP	.											.	RAB21	17	.	0			c.G34A						PASS	.						8.0	6.0	7.0					12																	72148943		1935	3805	5740	SO:0001583	missense	23011	exon1			GGGGCGGCGGCGG	AF091035	CCDS9003.1	12q21.1	2014-09-04			ENSG00000080371	ENSG00000080371		"""RAB, member RAS oncogene"""	18263	protein-coding gene	gene with protein product		612398				10887961, 11697911, 16754960	Standard	NM_014999		Approved	KIAA0118	uc001swt.3	Q9UL25	OTTHUMG00000169572	ENST00000261263.3:c.34G>A	12.37:g.72148943G>A	ENSP00000261263:p.Ala12Thr	0.0	0.0	.		11.0	9.0	0.818182	NM_014999	Q14466|Q569H3	Missense_Mutation	SNP	ENST00000261263.3	37	CCDS9003.1	.	.	.	.	.	.	.	.	.	.	G	8.412	0.844345	0.16963	.	.	ENSG00000080371	ENST00000261263	T	0.67865	-0.29	3.75	3.75	0.43078	.	0.068284	0.64402	D	0.000019	T	0.64681	0.2620	L	0.28504	0.86	0.46654	D	0.999142	D	0.57571	0.98	P	0.57009	0.811	T	0.59026	-0.7531	10	0.15952	T	0.53	-8.1075	13.8606	0.63557	0.0:0.0:1.0:0.0	.	12	Q9UL25	RAB21_HUMAN	T	12	ENSP00000261263:A12T	ENSP00000261263:A12T	A	+	1	0	RAB21	70435210	1.000000	0.71417	0.997000	0.53966	0.253000	0.25986	4.732000	0.62029	2.072000	0.62099	0.557000	0.71058	GCG	.	.	none		0.741	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1		
JAKMIP1	152789	hgsc.bcm.edu	37	4	6062160	6062160	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:6062160C>T	ENST00000282924.5	-	11	2120	c.1635G>A	c.(1633-1635)gaG>gaA	p.E545E	JAKMIP1_ENST00000457227.2_5'Flank|JAKMIP1_ENST00000409021.3_Silent_p.E545E|JAKMIP1_ENST00000410077.2_Silent_p.E380E|JAKMIP1_ENST00000409371.3_Silent_p.E360E|JAKMIP1_ENST00000409831.1_Silent_p.E545E	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	545	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCTGTCCCTTCTCAACCAGTA	0.537																																					p.E545E		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G1635A						PASS	.						214.0	201.0	206.0					4																	6062160		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon11			TCCCTTCTCAACC	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1635G>A	4.37:g.6062160C>T		92.0	0.0	0		83.0	29.0	0.349398	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	37	CCDS3385.1																																																																																			.	.	none		0.537	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
KCNH7	90134	hgsc.bcm.edu	37	2	163228507	163228507	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:163228507A>C	ENST00000332142.5	-	16	3522	c.3423T>G	c.(3421-3423)acT>acG	p.T1141T		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	1141					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TTAAAAGTGAAGTCAAGTTGT	0.388																																					p.T1141T	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											KCNH7,NS,carcinoma,0,1	KCNH7	378	1	0			c.T3423G						PASS	.						86.0	84.0	85.0					2																	163228507		2203	4300	6503	SO:0001819	synonymous_variant	90134	exon16			AAGTGAAGTCAAG	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.3423T>G	2.37:g.163228507A>C		117.0	0.0	0		77.0	33.0	0.428571	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	CCDS2219.1																																																																																			.	.	none		0.388	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272	
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62194238C>T	ENST00000467148.1	-	8	6006	c.5937G>A	c.(5935-5937)ccG>ccA	p.P1979P	HELZ2_ENST00000427522.2_Silent_p.P1410P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1979					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCTGCCCCTGCGGCGTCCGTG	0.657													C|||	71	0.0141773	0.0008	0.0303	5008	,	,		15702	0.001		0.0408	False		,,,				2504	0.0072				p.P1979P		Atlas-SNP	.											.	.	.	.	0			c.G5937A						PASS	.	C	,	23,4271		0,23,2124	10.0	11.0	11.0		5937,4230	-9.2	0.0	20	dbSNP_126	11	243,8151		3,237,3957	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	3,260,6081	TT,TC,CC		2.8949,0.5356,2.0965	,	1979/2650,1410/2081	62194238	266,12422	2147	4197	6344	SO:0001819	synonymous_variant	85441	exon9			CCCCTGCGGCGTC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.5937G>A	20.37:g.62194238C>T		67.0	0.0	0		70.0	33.0	0.471429	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.984;T|0.016	0.016	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
SMYD1	150572	hgsc.bcm.edu	37	2	88387508	88387508	+	Silent	SNP	C	C	A	rs113636517	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:88387508C>A	ENST00000419482.2	+	3	527	c.442C>A	c.(442-444)Cgg>Agg	p.R148R	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.R148R	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	148	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						GAAGGACCTGCGGGTGGACGT	0.627													C|||	6	0.00119808	0.0	0.0	5008	,	,		18746	0.0		0.003	False		,,,				2504	0.0031				p.R148R		Atlas-SNP	.											.	SMYD1	95	.	0			c.C442A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	123.0	92.0	103.0		442	4.8	0.9	2	dbSNP_132	103	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous	SMYD1	NM_198274.3		0,77,6426	AA,AC,CC		0.7907,0.2043,0.592		148/491	88387508	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon3			GACCTGCGGGTGG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.442C>A	2.37:g.88387508C>A		239.0	1.0	0.0041841		191.0	132.0	0.691099	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			C|0.995;A|0.005	0.005	strong		0.627	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
RBM44	375316	hgsc.bcm.edu	37	2	238725962	238725962	+	Missense_Mutation	SNP	G	G	A	rs182474506		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238725962G>A	ENST00000409864.1	+	3	657	c.403G>A	c.(403-405)Gat>Aat	p.D135N	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.D135N			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	134						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TTCAGAATTAGATCCTGAAGT	0.313													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.D135N		Atlas-SNP	.											.	RBM44	167	.	0			c.G403A						PASS	.	G	ASN/ASP	1,3595		0,1,1797	25.0	24.0	24.0		403	1.4	0.2	2		24	13,8105		0,13,4046	yes	missense	RBM44	NM_001080504.2	23	0,14,5843	AA,AG,GG		0.1601,0.0278,0.1195	benign	135/1053	238725962	14,11700	1798	4059	5857	SO:0001583	missense	375316	exon3			GAATTAGATCCTG	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.403G>A	2.37:g.238725962G>A	ENSP00000386727:p.Asp135Asn	103.0	0.0	0		99.0	44.0	0.444444	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	12.37	1.916209	0.33815	2.78E-4	0.001601	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.30182	1.54;1.54	5.47	1.35	0.21983	.	0.605422	0.15459	N	0.261208	T	0.23688	0.0573	L	0.54323	1.7	0.09310	N	1	B	0.28760	0.221	B	0.19148	0.024	T	0.15607	-1.0431	10	0.54805	T	0.06	-3.5583	5.6878	0.17813	0.1812:0.2994:0.5194:0.0	.	134	Q6ZP01	RBM44_HUMAN	N	135	ENSP00000321179:D135N;ENSP00000386727:D135N	ENSP00000321179:D135N	D	+	1	0	RBM44	238390701	0.795000	0.28851	0.183000	0.23137	0.182000	0.23217	0.220000	0.17660	-0.018000	0.14079	0.558000	0.71614	GAT	G|0.999;A|0.001	0.001	strong		0.313	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
DDX51	317781	hgsc.bcm.edu	37	12	132625027	132625027	+	Silent	SNP	G	G	A	rs61942919	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132625027G>A	ENST00000397333.3	-	11	1652	c.1614C>T	c.(1612-1614)cgC>cgT	p.R538R		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	538	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CAGGCCCGTAGCGCGAGGAGA	0.617													G|||	29	0.00579073	0.0	0.0086	5008	,	,		16503	0.0		0.004	False		,,,				2504	0.0194				p.R538R		Atlas-SNP	.											DDX51,NS,carcinoma,-1,1	DDX51	33	1	0			c.C1614T						PASS	.	G		3,4217		0,3,2107	72.0	83.0	79.0		1614	4.1	0.9	12	dbSNP_129	79	58,8392		0,58,4167	no	coding-synonymous	DDX51	NM_175066.3		0,61,6274	AA,AG,GG		0.6864,0.0711,0.4815		538/667	132625027	61,12609	2110	4225	6335	SO:0001819	synonymous_variant	317781	exon11			CCCGTAGCGCGAG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1614C>T	12.37:g.132625027G>A		87.0	0.0	0		84.0	32.0	0.380952	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.995;A|0.005	0.005	strong		0.617	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
ZNF131	7690	hgsc.bcm.edu	37	5	43173541	43173541	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:43173541C>T	ENST00000399534.1	+	6	1220	c.1176C>T	c.(1174-1176)taC>taT	p.Y392Y	ZNF131_ENST00000505606.2_Silent_p.Y358Y|ZNF131_ENST00000509156.1_Silent_p.Y392Y|ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000306938.4_Silent_p.Y358Y|ZNF131_ENST00000509634.1_Silent_p.Y358Y			P52739	ZN131_HUMAN	zinc finger protein 131	392					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						AGAAGCTCTACGAATGCCAGG	0.418																																					p.Y358Y		Atlas-SNP	.											.	ZNF131	51	.	0			c.C1074T						PASS	.						70.0	67.0	68.0					5																	43173541		1917	4148	6065	SO:0001819	synonymous_variant	7690	exon7			GCTCTACGAATGC	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"""Zinc fingers, C2H2-type"", ""-"", ""BTB/POZ domain containing"""	12915	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 35"""	604073	"""zinc finger protein 131 (clone pHZ-10)"""				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.1176C>T	5.37:g.43173541C>T		87.0	0.0	0		85.0	38.0	0.447059	NM_003432	B4DRL3|Q6PIF0	Silent	SNP	ENST00000399534.1	37																																																																																				.	.	none		0.418	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432	
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:101804366T>C	ENST00000375001.3	+	24	2974	c.2551T>C	c.(2551-2553)Ttt>Ctt	p.F851L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	851	Collagen-like 3.|Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TTTACCTGGCTTTCCAGGACT	0.423													T|||	16	0.00319489	0.0015	0.0058	5008	,	,		17702	0.0		0.008	False		,,,				2504	0.002				p.F851L		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2551C						PASS	.	T	LEU/PHE	11,4395	17.9+/-39.9	0,11,2192	95.0	103.0	100.0		2551	5.9	1.0	9	dbSNP_126	100	108,8492	57.2+/-118.5	0,108,4192	yes	missense	COL15A1	NM_001855.3	22	0,119,6384	CC,CT,TT		1.2558,0.2497,0.915	probably-damaging	851/1389	101804366	119,12887	2203	4300	6503	SO:0001583	missense	1306	exon24			CCTGGCTTTCCAG	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2551T>C	9.37:g.101804366T>C	ENSP00000364140:p.Phe851Leu	54.0	0.0	0		67.0	37.0	0.552239	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	11	0.005036630036630037	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	19.54	3.846980	0.71603	0.002497	0.012558	ENSG00000204291	ENST00000375001	D	0.93133	-3.17	5.92	5.92	0.95590	.	0.251977	0.40818	N	0.001007	D	0.88815	0.6539	N	0.10760	0.04	0.40583	D	0.981411	D	0.69078	0.997	D	0.77004	0.989	D	0.88409	0.3020	10	0.20046	T	0.44	-12.7642	12.7552	0.57331	0.0:0.0:0.0:1.0	rs35901514	851	P39059	COFA1_HUMAN	L	851	ENSP00000364140:F851L	ENSP00000364140:F851L	F	+	1	0	COL15A1	100844187	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	2.145000	0.42207	2.270000	0.75569	0.459000	0.35465	TTT	T|0.993;C|0.007	0.007	strong		0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
CARD11	84433	hgsc.bcm.edu	37	7	2983886	2983886	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2983886T>A	ENST00000396946.4	-	5	1047	c.644A>T	c.(643-645)aAg>aTg	p.K215M	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGCCATGTTCTTCTCCTCACT	0.572			Mis		DLBCL																																p.K215M		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,colon,carcinoma,-1,6	CARD11	339	6	0			c.A644T						PASS	.						187.0	114.0	139.0					7																	2983886		2203	4300	6503	SO:0001583	missense	84433	exon5			ATGTTCTTCTCCT	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.644A>T	7.37:g.2983886T>A	ENSP00000380150:p.Lys215Met	174.0	0.0	0		199.0	88.0	0.442211	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.62	3.662813	0.67700	.	.	ENSG00000198286	ENST00000396946	T	0.38722	1.12	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	L	0.57536	1.79	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.63664	-0.6586	10	0.72032	D	0.01	-28.1579	13.4982	0.61438	0.0:0.0:0.0:1.0	.	215	Q9BXL7	CAR11_HUMAN	M	215	ENSP00000380150:K215M	ENSP00000380150:K215M	K	-	2	0	CARD11	2950412	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	5.720000	0.68470	1.650000	0.50662	0.459000	0.35465	AAG	.	.	none		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
USP13	8975	hgsc.bcm.edu	37	3	179424788	179424788	+	Missense_Mutation	SNP	T	T	C	rs141550831	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:179424788T>C	ENST00000263966.3	+	5	1015	c.544T>C	c.(544-546)Tgg>Cgg	p.W182R	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Missense_Mutation_p.W117R	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	182					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CCCAGACACGTGGGAAAATGA	0.423																																					p.W182R		Atlas-SNP	.											USP13,NS,carcinoma,-1,1	USP13	117	1	0			c.T544C						PASS	.	T	ARG/TRP	2,4404	4.2+/-10.8	0,2,2201	102.0	92.0	95.0		544	6.0	1.0	3	dbSNP_134	95	4,8596	3.7+/-12.6	0,4,4296	yes	missense	USP13	NM_003940.2	101	0,6,6497	CC,CT,TT		0.0465,0.0454,0.0461	probably-damaging	182/864	179424788	6,13000	2203	4300	6503	SO:0001583	missense	8975	exon5			GACACGTGGGAAA	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.544T>C	3.37:g.179424788T>C	ENSP00000263966:p.Trp182Arg	157.0	0.0	0		150.0	89.0	0.593333	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.717237	0.89205	4.54E-4	4.65E-4	ENSG00000058056	ENST00000263966;ENST00000496897	T;T	0.35789	1.31;1.29	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.64034	0.2562	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.68515	-0.5388	10	0.87932	D	0	-10.5405	16.5494	0.84464	0.0:0.0:0.0:1.0	.	182;182	Q92995;A8K2S3	UBP13_HUMAN;.	R	182;117	ENSP00000263966:W182R;ENSP00000417146:W117R	ENSP00000263966:W182R	W	+	1	0	USP13	180907482	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.698000	0.84413	2.299000	0.77371	0.528000	0.53228	TGG	T|0.999;C|0.001	0.001	strong		0.423	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		
SEL1L2	80343	hgsc.bcm.edu	37	20	13912308	13912308	+	Missense_Mutation	SNP	C	C	T	rs143129534	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13912308C>T	ENST00000284951.5	-	3	298	c.224G>A	c.(223-225)cGt>cAt	p.R75H	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.R75H			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	75						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TCTTATTTTACGTTGATTCTT	0.244													C|||	36	0.0071885	0.0008	0.0101	5008	,	,		15470	0.0		0.0219	False		,,,				2504	0.0061				p.R75H		Atlas-SNP	.											SEL1L2,colon,carcinoma,-1,1	SEL1L2	103	1	0			c.G224A						scavenged	.	C	HIS/ARG	12,3540		0,12,1764	57.0	50.0	52.0		224	-5.1	0.0	20	dbSNP_134	52	162,7902		1,160,3871	no	missense	SEL1L2	NM_025229.1	29	1,172,5635	TT,TC,CC		2.0089,0.3378,1.4979	benign	75/689	13912308	174,11442	1776	4032	5808	SO:0001583	missense	80343	exon3			ATTTTACGTTGAT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.224G>A	20.37:g.13912308C>T	ENSP00000284951:p.Arg75His	98.0	1.0	0.0102041		108.0	40.0	0.37037	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		24	0.01098901098901099	0	0.0	5	0.013812154696132596	0	0.0	19	0.025065963060686015	C	2.707	-0.269735	0.05716	0.003378	0.020089	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23147	1.92;2.23	5.11	-5.07	0.02938	.	1.668320	0.03077	N	0.157986	T	0.03695	0.0105	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25847	-1.0120	10	0.14252	T	0.57	3.976	12.3194	0.54977	0.0:0.6944:0.0:0.3056	.	75;75	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	H	75	ENSP00000367312:R75H;ENSP00000284951:R75H	ENSP00000284951:R75H	R	-	2	0	SEL1L2	13860308	0.016000	0.18221	0.000000	0.03702	0.311000	0.27955	-1.651000	0.01989	-0.970000	0.03569	-0.290000	0.09829	CGT	C|0.988;T|0.012	0.012	strong		0.244	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
ARHGAP18	93663	hgsc.bcm.edu	37	6	129929191	129929191	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:129929191A>C	ENST00000368149.2	-	9	1217	c.1129T>G	c.(1129-1131)Tgc>Ggc	p.C377G		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18											NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		AGTTCTTGGCAAAGATTCTGA	0.373																																					p.C377G		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.T1129G						PASS	.						46.0	47.0	47.0					6																	129929191		2203	4300	6503	SO:0001583	missense	93663	exon9			CTTGGCAAAGATT	AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"""Rho GTPase activating proteins"""	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.1129T>G	6.37:g.129929191A>C	ENSP00000357131:p.Cys377Gly	25.0	0.0	0		38.0	9.0	0.236842	NM_033515		Missense_Mutation	SNP	ENST00000368149.2	37	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.419687	0.62622	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.84	4.67	0.58626	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.090614	0.85682	D	0.000000	T	0.58595	0.2133	M	0.72353	2.195	0.58432	D	0.999995	D;P	0.65815	0.995;0.823	P;P	0.54544	0.755;0.565	T	0.62263	-0.6891	8	.	.	.	.	12.1678	0.54139	0.9322:0.0:0.0678:0.0	.	377;377	A9UK01;Q8N392	.;RHG18_HUMAN	G	332;377	.	.	C	-	1	0	ARHGAP18	129970884	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.300000	0.72776	2.228000	0.72767	0.533000	0.62120	TGC	.	.	none		0.373	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515	
NACAD	23148	hgsc.bcm.edu	37	7	45120282	45120282	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:45120282C>T	ENST00000490531.2	-	7	4650	c.4631G>A	c.(4630-4632)cGg>cAg	p.R1544Q		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1544					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						TCTCAGAGCCCGCACGGCCTT	0.632																																					p.R1544Q		Atlas-SNP	.											.	NACAD	44	.	0			c.G4631A						PASS	.						147.0	156.0	153.0					7																	45120282		692	1591	2283	SO:0001583	missense	23148	exon7			AGAGCCCGCACGG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.4631G>A	7.37:g.45120282C>T	ENSP00000420477:p.Arg1544Gln	131.0	0.0	0		115.0	74.0	0.643478	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082371	0.55861	.	.	ENSG00000136274	ENST00000490531	T	0.12984	2.63	4.57	1.69	0.24217	.	0.066288	0.64402	N	0.000008	T	0.18759	0.0450	L	0.52266	1.64	0.52501	D	0.999952	D	0.56035	0.974	P	0.51777	0.679	T	0.01326	-1.1384	10	0.66056	D	0.02	-17.4362	8.9669	0.35883	0.0:0.7418:0.0:0.2582	.	1544	O15069	NACAD_HUMAN	Q	1544	ENSP00000420477:R1544Q	ENSP00000420477:R1544Q	R	-	2	0	NACAD	45086807	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	2.400000	0.44504	0.553000	0.29044	0.289000	0.19496	CGG	.	.	none		0.632	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
PARP11	57097	hgsc.bcm.edu	37	12	3931308	3931308	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3931308G>A	ENST00000228820.4	-	5	504	c.360C>T	c.(358-360)aaC>aaT	p.N120N	PARP11_ENST00000427057.2_Silent_p.N39N|PARP11_ENST00000397096.2_Silent_p.N113N|PARP11_ENST00000476985.1_5'Flank|PARP11_ENST00000447133.3_Silent_p.N39N	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	113	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			GGATGGCCTCGTTTTCACAGA	0.388																																					p.N120N		Atlas-SNP	.											.	PARP11	39	.	0			c.C360T						PASS	.						106.0	96.0	99.0					12																	3931308		2203	4300	6503	SO:0001819	synonymous_variant	57097	exon5			GGCCTCGTTTTCA	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"""Poly (ADP-ribose) polymerases"""	1186	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 6"""	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.360C>T	12.37:g.3931308G>A		87.0	0.0	0		93.0	12.0	0.129032	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Silent	SNP	ENST00000228820.4	37	CCDS8523.2																																																																																			.	.	none		0.388	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1		
ENPP2	5168	hgsc.bcm.edu	37	8	120569823	120569823	+	Missense_Mutation	SNP	G	G	A	rs61738778	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:120569823G>A	ENST00000075322.6	-	25	2588	c.2530C>T	c.(2530-2532)Cgc>Tgc	p.R844C	ENPP2_ENST00000427067.2_Missense_Mutation_p.R865C|ENPP2_ENST00000259486.6_Missense_Mutation_p.R896C|ENPP2_ENST00000522167.1_Missense_Mutation_p.R479C|ENPP2_ENST00000522826.1_Missense_Mutation_p.R869C	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	844	Required for secretion. {ECO:0000250}.				cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GGGTAGCTGCGGCTGGTCTTT	0.463													G|||	5	0.000998403	0.0	0.0	5008	,	,		17365	0.0		0.004	False		,,,				2504	0.001				p.R896C	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.C2686T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	187.0	174.0	179.0		2530,2605,2686	6.0	1.0	8	dbSNP_129	179	56,8544	36.4+/-91.3	0,56,4244	yes	missense,missense,missense	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	180,180,180	0,61,6442	AA,AG,GG		0.6512,0.1135,0.469	probably-damaging,probably-damaging,probably-damaging	844/864,869/889,896/916	120569823	61,12945	2203	4300	6503	SO:0001583	missense	5168	exon26			AGCTGCGGCTGGT	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2530C>T	8.37:g.120569823G>A	ENSP00000075322:p.Arg844Cys	120.0	0.0	0		106.0	51.0	0.481132	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	22.7	4.328424	0.81690	0.001135	0.006512	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	6.02	6.02	0.97574	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.049096	0.85682	D	0.000000	T	0.74884	0.3775	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.76071	0.987;0.976;0.939;0.978;0.984	T	0.77373	-0.2612	10	0.62326	D	0.03	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	382;869;844;896;479	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	C	896;865;479;869;844	ENSP00000259486:R896C;ENSP00000403315:R865C;ENSP00000429476:R479C;ENSP00000428291:R869C;ENSP00000075322:R844C	ENSP00000075322:R844C	R	-	1	0	ENPP2	120639004	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.287000	0.65645	2.865000	0.98341	0.655000	0.94253	CGC	G|0.996;A|0.004	0.004	strong		0.463	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Intron	SNP	T	T	G	rs143144671	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.E40A|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		ATCCAGCCATTCCTGGGTACC	0.522													t|||	4	0.000798722	0.0	0.0029	5008	,	,		18122	0.0		0.002	False		,,,				2504	0.0				p.E40A		Atlas-SNP	.											.	ETFB	46	.	0			c.A119C						PASS	.	T	ALA/GLU,	3,4403	6.2+/-15.9	0,3,2200	88.0	83.0	85.0		119,	-3.9	0.0	19	dbSNP_134	85	31,8569	21.6+/-65.8	0,31,4269	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	107,	0,34,6469	GG,GT,TT		0.3605,0.0681,0.2614	possibly-damaging,	40/347,	51857774	34,12972	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			AGCCATTCCTGGG	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-212A>C	19.37:g.51857774T>G		67.0	0.0	0		71.0	42.0	0.591549	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	t	12.37	1.918726	0.33908	6.81E-4	0.003605	ENSG00000105379	ENST00000354232	D	0.85339	-1.97	2.49	-3.88	0.04205	.	.	.	.	.	T	0.68430	0.3000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50558	-0.8814	7	.	.	.	.	4.1225	0.10112	0.0:0.1914:0.3562:0.4524	.	40	P38117-2	.	A	40	ENSP00000346173:E40A	.	E	-	2	0	ETFB	56549586	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.697000	0.05098	-1.056000	0.03205	-0.319000	0.08680	GAA	T|0.998;G|0.002	0.002	strong		0.522	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
WNK2	65268	hgsc.bcm.edu	37	9	96030957	96030957	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96030957A>G	ENST00000297954.4	+	18	3962	c.3962A>G	c.(3961-3963)cAc>cGc	p.H1321R	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.H933R|WNK2_ENST00000349097.3_Missense_Mutation_p.H933R|WNK2_ENST00000395477.2_Missense_Mutation_p.H1321R|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1321					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GTGGCTGAGCACCCCGCCCCC	0.632																																					p.H1321R		Atlas-SNP	.											.	WNK2	277	.	0			c.A3962G						PASS	.						56.0	47.0	50.0					9																	96030957		2203	4300	6503	SO:0001583	missense	65268	exon18			CTGAGCACCCCGC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3962A>G	9.37:g.96030957A>G	ENSP00000297954:p.His1321Arg	116.0	0.0	0		95.0	27.0	0.284211	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.28|18.28	3.588088|3.588088	0.66105|0.66105	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.33865|.	1.39;1.39;1.39;1.39|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.185244|.	0.47455|.	D|.	0.000234|.	T|T	0.36908|0.36908	0.0984|0.0984	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D;B;B;D|.	0.63880|.	0.99;0.183;0.418;0.993|.	P;B;B;D|.	0.72338|.	0.882;0.026;0.058;0.977|.	T|T	0.33137|0.33137	-0.9880|-0.9880	10|5	0.27785|.	T|.	0.31|.	.|.	12.2871|12.2871	0.54797|0.54797	0.8587:0.1413:0.0:0.0|0.8587:0.1413:0.0:0.0	.|.	1321;924;1321;1321|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	R|A	1321;1321;933;933|1317;118	ENSP00000297954:H1321R;ENSP00000378860:H1321R;ENSP00000297876:H933R;ENSP00000411181:H933R|.	ENSP00000297954:H1321R|.	H|T	+|+	2|1	0|0	WNK2|WNK2	95070778|95070778	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.675000|0.675000	0.39556|0.39556	3.831000|3.831000	0.55776|0.55776	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.	.	none		0.632	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
OTC	5009	hgsc.bcm.edu	37	X	38262964	38262964	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:38262964G>A	ENST00000039007.4	+	6	786	c.634G>A	c.(634-636)Gga>Aga	p.G212R	TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	212					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	AGCGAAATTCGGAATGCACCT	0.463																																					p.G212R		Atlas-SNP	.											.	OTC	60	.	0			c.G634A						PASS	.						105.0	84.0	91.0					X																	38262964		2202	4300	6502	SO:0001583	missense	5009	exon6			AAATTCGGAATGC	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.634G>A	X.37:g.38262964G>A	ENSP00000039007:p.Gly212Arg	47.0	0.0	0		59.0	18.0	0.305085	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	g	31	5.090646	0.94149	.	.	ENSG00000036473	ENST00000039007	D	0.99329	-5.75	5.91	5.91	0.95273	Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97657	1.0158	10	0.87932	D	0	-23.1274	19.2113	0.93757	0.0:0.0:1.0:0.0	.	212	P00480	OTC_HUMAN	R	212	ENSP00000039007:G212R	ENSP00000039007:G212R	G	+	1	0	OTC	38147908	1.000000	0.71417	0.597000	0.28824	0.891000	0.51852	9.417000	0.97391	2.488000	0.83962	0.594000	0.82650	GGA	.	.	none		0.463	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
LTB	4050	hgsc.bcm.edu	37	6	31549604	31549604	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31549604G>A	ENST00000429299.2	-	2	202	c.195C>T	c.(193-195)gcC>gcT	p.A65A	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	65				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GTCCTTGCTGGGCCTGTGCCC	0.617																																					p.A65A		Atlas-SNP	.											.	LTB	19	.	0			c.C195T						PASS	.						91.0	100.0	97.0					6																	31549604		1510	2708	4218	SO:0001819	synonymous_variant	4050	exon2			TTGCTGGGCCTGT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.195C>T	6.37:g.31549604G>A		69.0	0.0	0		80.0	27.0	0.3375	NM_002341	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																			.	.	none		0.617	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
CHST1	8534	hgsc.bcm.edu	37	11	45671241	45671241	+	Silent	SNP	C	C	G	rs7115779	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:45671241C>G	ENST00000308064.2	-	4	1903	c.1233G>C	c.(1231-1233)tcG>tcC	p.S411S	RP11-495O11.1_ENST00000525563.1_RNA|CHST1_ENST00000533673.1_5'Flank	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	411					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		GCCCGGGTCACGAGAAGGGGC	0.627													C|||	12	0.00239617	0.0	0.0014	5008	,	,		14438	0.0		0.007	False		,,,				2504	0.0041				p.S411S		Atlas-SNP	.											CHST1,colon,adenoma,0,1	CHST1	81	1	0			c.G1233C						PASS	.	C		5,4395		0,5,2195	32.0	40.0	38.0		1233	4.4	1.0	11	dbSNP_116	38	30,8532		0,30,4251	yes	coding-synonymous	CHST1	NM_003654.5		0,35,6446	GG,GC,CC		0.3504,0.1136,0.27		411/412	45671241	35,12927	2200	4281	6481	SO:0001819	synonymous_variant	8534	exon4			GGGTCACGAGAAG	U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"""Sulfotransferases, membrane-bound"""	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.1233G>C	11.37:g.45671241C>G		27.0	0.0	0		25.0	11.0	0.44	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	37	CCDS7913.1																																																																																			C|0.989;G|0.011	0.011	strong		0.627	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
MRPL38	64978	hgsc.bcm.edu	37	17	73895744	73895744	+	Missense_Mutation	SNP	G	G	A	rs1128878		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73895744G>A	ENST00000309352.3	-	7	1259	c.722C>T	c.(721-723)cCg>cTg	p.P241L	MRPL38_ENST00000409963.3_Missense_Mutation_p.P57L|RP11-552F3.10_ENST00000587267.1_RNA|MRPL38_ENST00000585475.1_5'Flank|TRIM65_ENST00000269383.3_5'Flank	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	241						mitochondrion (GO:0005739)|ribosome (GO:0005840)				ovary(1)|pancreas(1)|prostate(2)|skin(1)	5			all cancers(21;0.000154)|Epithelial(20;0.000156)|BRCA - Breast invasive adenocarcinoma(9;0.00936)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCGGTTACCCGGGATGTTGGT	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		17869	0.0		0.001	False		,,,				2504	0.0				p.P241L		Atlas-SNP	.											.	MRPL38	26	.	0			c.C722T						PASS	.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	37.0	38.0	38.0		722	5.9	1.0	17	dbSNP_86	38	11,8583	8.4+/-32.0	0,11,4286	yes	missense	MRPL38	NM_032478.3	98	0,13,6487	AA,AG,GG		0.128,0.0454,0.1	probably-damaging	241/381	73895744	13,12987	2203	4297	6500	SO:0001583	missense	64978	exon7			TTACCCGGGATGT	AB051345	CCDS11733.2	17q23-q25	2012-09-13			ENSG00000204316	ENSG00000204316		"""Mitochondrial ribosomal proteins / large subunits"""	14033	protein-coding gene	gene with protein product		611844				11543634	Standard	NM_032478		Approved	RPML3, MRP-L3, HSPC262, MGC4810	uc010wso.1	Q96DV4	OTTHUMG00000152977	ENST00000309352.3:c.722C>T	17.37:g.73895744G>A	ENSP00000308275:p.Pro241Leu	54.0	0.0	0		57.0	21.0	0.368421	NM_032478	B3KN96|Q96Q66|Q9P0B9	Missense_Mutation	SNP	ENST00000309352.3	37	CCDS11733.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.459407	0.96240	4.54E-4	0.00128	ENSG00000204316	ENST00000309352;ENST00000409963	T;T	0.59224	0.48;0.28	5.87	5.87	0.94306	.	0.048517	0.85682	N	0.000000	T	0.81054	0.4743	H	0.97103	3.94	0.80722	D	1	D	0.63046	0.992	P	0.52514	0.701	D	0.87262	0.2280	10	0.87932	D	0	-13.2193	20.2144	0.98291	0.0:0.0:1.0:0.0	rs1128878;rs17352818	241	Q96DV4	RM38_HUMAN	L	241;57	ENSP00000308275:P241L;ENSP00000387085:P57L	ENSP00000308275:P241L	P	-	2	0	MRPL38	71407339	1.000000	0.71417	0.969000	0.41365	0.933000	0.57130	8.872000	0.92352	2.791000	0.96007	0.511000	0.50034	CCG	G|0.999;A|0.001	0.001	strong		0.612	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1	NM_032478	
LEPR	3953	hgsc.bcm.edu	37	1	66102617	66102617	+	Silent	SNP	A	A	G	rs61781316	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:66102617A>G	ENST00000349533.6	+	20	3602	c.3417A>G	c.(3415-3417)gcA>gcG	p.A1139A	LEPR_ENST00000406510.3_Silent_p.A206A	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AGACTTTTGCATCTTACATGC	0.383													A|||	3	0.000599042	0.0	0.0	5008	,	,		17998	0.0		0.003	False		,,,				2504	0.0				p.A1139A		Atlas-SNP	.											.	LEPR	284	.	0			c.A3417G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	73.0	74.0	74.0		3417	-8.3	0.3	1	dbSNP_129	74	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous	LEPR	NM_002303.5		0,49,6454	GG,GA,AA		0.5465,0.0454,0.3767		1139/1166	66102617	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	3953	exon20			TTTTGCATCTTAC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3417A>G	1.37:g.66102617A>G		71.0	0.0	0		44.0	17.0	0.386364	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																			A|0.997;G|0.003	0.003	strong		0.383	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
Unknown	0	hgsc.bcm.edu	37	11	124096271	124096271	+	IGR	SNP	A	A	G	rs201854907	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124096271A>G								OR10D3 (39319 upstream) : OR8G1 (24151 downstream)																							TGTGTTTTATACTATTGTTGT	0.448																																					p.T292A		Atlas-SNP	.											.	.	.	.	0			c.A874G						PASS	.	A	ALA/THR	4,3862		0,4,1929	73.0	68.0	69.0		874	1.3	0.0	11		69	24,8280		0,24,4128	no	missense	OR8G2	NM_001007249.1	58	0,28,6057	GG,GA,AA		0.289,0.1035,0.2301	possibly-damaging	292/305	124096271	28,12142	1933	4152	6085	SO:0001628	intergenic_variant	26492	exon1			TTTTATACTATTG																													11.37:g.124096271A>G		175.0	0.0	0		201.0	16.0	0.079602	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.996;G|0.005	0.005	strong	0	0.448								
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						PASS	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42.0	41.0	41.0		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	66.0	0.0	0		46.0	25.0	0.543478	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
CD83	9308	hgsc.bcm.edu	37	6	14118297	14118297	+	Splice_Site	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:14118297G>A	ENST00000379153.3	+	2	324		c.e2+1			NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule						defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				CTGGGTCAAGGTAGGTGCTGC	0.642																																					.		Atlas-SNP	.											.	CD83	23	.	0			c.153+1G>A						PASS	.						22.0	22.0	22.0					6																	14118297		2203	4300	6503	SO:0001630	splice_region_variant	9308	exon2			GTCAAGGTAGGTG	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.153+1G>A	6.37:g.14118297G>A		29.0	0.0	0		32.0	10.0	0.3125	NM_001040280	Q5THX9	Splice_Site	SNP	ENST00000379153.3	37	CCDS4532.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.732915	0.30684	.	.	ENSG00000112149	ENST00000379153	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6741	0.56884	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD83	14226276	1.000000	0.71417	0.998000	0.56505	0.141000	0.21300	4.759000	0.62227	2.031000	0.59945	0.491000	0.48974	.	.	.	none		0.642	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		Intron
NOP9	161424	hgsc.bcm.edu	37	14	24771172	24771172	+	Splice_Site	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24771172G>A	ENST00000267425.3	+	4	903	c.810G>A	c.(808-810)gtG>gtA	p.V270V	NOP9_ENST00000396802.3_Splice_Site_p.V270V|DHRS1_ENST00000396813.1_5'Flank|DHRS1_ENST00000288111.7_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	270							poly(A) RNA binding (GO:0044822)										TCTCCACAGTGTTTATCACTG	0.458																																					p.V270V		Atlas-SNP	.											.	.	.	.	0			c.G810A						PASS	.						219.0	233.0	228.0					14																	24771172		2203	4300	6503	SO:0001630	splice_region_variant	161424	exon4			CACAGTGTTTATC		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.809-1G>A	14.37:g.24771172G>A		75.0	0.0	0		58.0	11.0	0.189655	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			.	.	none		0.458	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		Silent
DUSP2	1844	hgsc.bcm.edu	37	2	96810556	96810556	+	Missense_Mutation	SNP	G	G	A	rs537374232		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:96810556G>A	ENST00000288943.4	-	2	539	c.454C>T	c.(454-456)Ccg>Tcg	p.P152S	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	152					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				CCTGTTGGCGGCAGCGCAGGG	0.662													g|||	1	0.000199681	0.0008	0.0	5008	,	,		11061	0.0		0.0	False		,,,				2504	0.0				p.P152S		Atlas-SNP	.											DUSP2,NS,carcinoma,+2,1	DUSP2	20	1	0			c.C454T						PASS	.						11.0	16.0	14.0					2																	96810556		2150	4241	6391	SO:0001583	missense	1844	exon2			TTGGCGGCAGCGC	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.454C>T	2.37:g.96810556G>A	ENSP00000288943:p.Pro152Ser	92.0	0.0	0		76.0	9.0	0.118421	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	8.217	0.801609	0.16397	.	.	ENSG00000158050	ENST00000288943	T	0.02446	4.29	4.3	-1.0	0.10196	.	0.865607	0.10283	N	0.693284	T	0.01421	0.0046	N	0.12443	0.215	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49331	-0.8951	10	0.11794	T	0.64	.	2.8978	0.05696	0.2993:0.0:0.373:0.3277	.	152	Q05923	DUS2_HUMAN	S	152	ENSP00000288943:P152S	ENSP00000288943:P152S	P	-	1	0	DUSP2	96174283	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.181000	0.03085	-0.453000	0.07076	-0.509000	0.04479	CCG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
CYP3A4	1576	hgsc.bcm.edu	37	7	99358595	99358595	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358595C>T	ENST00000336411.2	-	12	1446	c.1263G>A	c.(1261-1263)aaG>aaA	p.K421K	CYP3A4_ENST00000354593.2_Silent_p.K271K	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	421					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	CCTTGTTCTTCTTGCTGAATC	0.413																																					p.K421K		Atlas-SNP	.											.	CYP3A4	56	.	0			c.G1263A						PASS	.						384.0	334.0	351.0					7																	99358595		2203	4300	6503	SO:0001819	synonymous_variant	1576	exon12			GTTCTTCTTGCTG	AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"""Cytochrome P450s"""	2637	protein-coding gene	gene with protein product		124010	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"""	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.1263G>A	7.37:g.99358595C>T		287.0	1.0	0.00348432		261.0	110.0	0.421456	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1		
WDTC1	23038	hgsc.bcm.edu	37	1	27631526	27631526	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27631526G>A	ENST00000319394.3	+	15	2213	c.1678G>A	c.(1678-1680)Ggc>Agc	p.G560S	WDTC1_ENST00000361771.3_Missense_Mutation_p.G559S	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	560					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CTCTGACGATGGCTCCTTCTT	0.592																																					p.G560S		Atlas-SNP	.											.	WDTC1	69	.	0			c.G1678A						PASS	.						75.0	61.0	65.0					1																	27631526		2203	4300	6503	SO:0001583	missense	23038	exon15			GACGATGGCTCCT	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.1678G>A	1.37:g.27631526G>A	ENSP00000317971:p.Gly560Ser	42.0	0.0	0		58.0	33.0	0.568965	NM_001276252	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	G	34	5.344179	0.95807	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	D;D	0.84146	-1.81;-1.81	4.82	4.82	0.62117	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	0.93429	0.7904	M	0.89163	3.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94408	0.7629	10	0.66056	D	0.02	.	17.0684	0.86565	0.0:0.0:1.0:0.0	.	560;559	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	S	560;559	ENSP00000317971:G560S;ENSP00000355317:G559S	ENSP00000317971:G560S	G	+	1	0	WDTC1	27504113	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.460000	0.80816	2.500000	0.84329	0.455000	0.32223	GGC	.	.	none		0.592	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
SLFN11	91607	hgsc.bcm.edu	37	17	33680127	33680127	+	Missense_Mutation	SNP	T	T	C	rs143643982		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33680127T>C	ENST00000394566.1	-	7	2226	c.1954A>G	c.(1954-1956)Aaa>Gaa	p.K652E	SLFN11_ENST00000308377.4_Missense_Mutation_p.K652E	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	652					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGGAAAGTTTTCCGGGTCTCT	0.383													T|||	1	0.000199681	0.0	0.0	5008	,	,		20114	0.0		0.001	False		,,,				2504	0.0				p.K652E		Atlas-SNP	.											.	SLFN11	112	.	0			c.A1954G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	0,4406		0,0,2203	79.0	78.0	79.0		1954,1954,1954,1954,1954	4.0	0.9	17	dbSNP_134	79	6,8594	1.2+/-3.3	0,6,4294	no	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	56,56,56,56,56	0,6,6497	CC,CT,TT		0.0698,0.0,0.0461	benign,benign,benign,benign,benign	652/902,652/902,652/902,652/902,652/902	33680127	6,13000	2203	4300	6503	SO:0001583	missense	91607	exon5			AAGTTTTCCGGGT	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1954A>G	17.37:g.33680127T>C	ENSP00000378067:p.Lys652Glu	43.0	0.0	0		47.0	26.0	0.553191	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	t	14.77	2.635559	0.47049	0.0	6.98E-4	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.84298	-1.83;-1.83	4.0	4.0	0.46444	Domain of unknown function DUF2075 (1);	0.126128	0.36101	N	0.002788	D	0.82449	0.5039	M	0.71296	2.17	0.23693	N	0.9971	B	0.21606	0.058	B	0.25405	0.06	T	0.71464	-0.4585	10	0.33940	T	0.23	.	9.4902	0.38955	0.0:0.0:0.0:1.0	.	652	Q7Z7L1	SLN11_HUMAN	E	652	ENSP00000312402:K652E;ENSP00000378067:K652E	ENSP00000312402:K652E	K	-	1	0	SLFN11	30704240	0.994000	0.37717	0.934000	0.37439	0.057000	0.15508	3.073000	0.50057	1.799000	0.52666	0.533000	0.62120	AAA	T|0.999;C|0.001	0.001	strong		0.383	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
FAF2	23197	hgsc.bcm.edu	37	5	175926010	175926010	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:175926010G>A	ENST00000261942.6	+	9	988	c.935G>A	c.(934-936)cGg>cAg	p.R312Q		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	312					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						AGAAAGAAACGGGAGGAGCGG	0.562																																					p.R312Q		Atlas-SNP	.											.	FAF2	38	.	0			c.G935A						PASS	.						89.0	93.0	91.0					5																	175926010		2203	4300	6503	SO:0001583	missense	23197	exon9			AGAAACGGGAGGA	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"""UBX domain containing"""	24666	protein-coding gene	gene with protein product	"""expressed in T cells and eosinophils in atopic dermatitis"", ""UBX domain protein 3B"""		"""UBX domain containing 8"""	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.935G>A	5.37:g.175926010G>A	ENSP00000261942:p.Arg312Gln	43.0	0.0	0		55.0	22.0	0.4	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Missense_Mutation	SNP	ENST00000261942.6	37	CCDS34296.1	.	.	.	.	.	.	.	.	.	.	G	8.857	0.946084	0.18356	.	.	ENSG00000113194	ENST00000261942	T	0.63096	-0.02	4.82	2.86	0.33363	.	0.193233	0.52532	D	0.000075	T	0.38692	0.1050	L	0.27975	0.815	0.37360	D	0.911177	B	0.15141	0.012	B	0.08055	0.003	T	0.18023	-1.0350	10	0.09338	T	0.73	-8.2648	4.4655	0.11687	0.4314:0.0:0.5686:0.0	.	312	Q96CS3	FAF2_HUMAN	Q	312	ENSP00000261942:R312Q	ENSP00000261942:R312Q	R	+	2	0	FAF2	175858616	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	3.577000	0.53885	1.249000	0.43950	0.561000	0.74099	CGG	.	.	none		0.562	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613	
CSMD1	64478	hgsc.bcm.edu	37	8	3253868	3253868	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:3253868A>T	ENST00000520002.1	-	18	2999	c.2444T>A	c.(2443-2445)gTc>gAc	p.V815D	CSMD1_ENST00000537824.1_Missense_Mutation_p.V814D|CSMD1_ENST00000400186.3_Missense_Mutation_p.V815D|CSMD1_ENST00000542608.1_Missense_Mutation_p.V814D|CSMD1_ENST00000539096.1_Missense_Mutation_p.V814D|CSMD1_ENST00000602557.1_Missense_Mutation_p.V815D|CSMD1_ENST00000602723.1_Missense_Mutation_p.V815D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	815	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCCATCTCTGACCTCCAAGGT	0.527																																					p.V814D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T2441A						PASS	.						49.0	63.0	58.0					8																	3253868		2163	4270	6433	SO:0001583	missense	64478	exon17			TCTCTGACCTCCA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2444T>A	8.37:g.3253868A>T	ENSP00000430733:p.Val815Asp	61.0	0.0	0		97.0	28.0	0.28866	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	A	15.68	2.905140	0.52333	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.3	5.3	0.74995	CUB (5);	0.073354	0.53938	D	0.000046	D	0.88142	0.6357	H	0.97611	4.04	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.91635	0.999;0.982	D	0.92260	0.5816	10	0.72032	D	0.01	.	15.2632	0.73640	1.0:0.0:0.0:0.0	.	815;815	E5RIG2;Q96PZ7	.;CSMD1_HUMAN	D	815;815;677;814;814;814	ENSP00000383047:V815D;ENSP00000430733:V815D;ENSP00000441462:V814D;ENSP00000446243:V814D;ENSP00000441675:V814D	ENSP00000320445:V677D	V	-	2	0	CSMD1	3241275	1.000000	0.71417	0.116000	0.21606	0.009000	0.06853	9.112000	0.94314	1.981000	0.57761	0.533000	0.62120	GTC	.	.	none		0.527	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
PRSS58	136541	hgsc.bcm.edu	37	7	141955390	141955390	+	Silent	SNP	C	C	T	rs145731516	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:141955390C>T	ENST00000552471.1	-	2	463	c.144G>A	c.(142-144)ccG>ccA	p.P48P	PRSS58_ENST00000547058.2_Silent_p.P48P			Q8IYP2	PRS58_HUMAN	protease, serine, 58	48	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						TCACCCAAAGCGGGTGGATCA	0.502													C|||	16	0.00319489	0.0	0.0029	5008	,	,		17941	0.0		0.0119	False		,,,				2504	0.002				p.P48P		Atlas-SNP	.											.	PRSS58	41	.	0			c.G144A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	79.0	77.0	77.0		144	-10.0	0.0	7	dbSNP_134	77	75,8525	44.5+/-102.8	0,75,4225	no	coding-synonymous	PRSS58	NM_001001317.3		0,83,6420	TT,TC,CC		0.8721,0.1816,0.6382		48/242	141955390	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon3			CCAAAGCGGGTGG		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"""Serine peptidases / Serine peptidases"""	39125	protein-coding gene	gene with protein product	"""trypsin X3"""						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.144G>A	7.37:g.141955390C>T		101.0	0.0	0		109.0	47.0	0.431193	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			C|0.994;T|0.006	0.006	strong		0.502	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
LYRM7	90624	hgsc.bcm.edu	37	5	130515811	130515811	+	Silent	SNP	G	G	A	rs113642581	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:130515811G>A	ENST00000379380.4	+	2	253	c.42G>A	c.(40-42)ctG>ctA	p.L14L	LYRM7_ENST00000507584.1_Silent_p.L14L|LYRM7_ENST00000510516.1_Silent_p.L14L	NM_181705.2	NP_859056.2	Q5U5X0	LYRM7_HUMAN	LYR motif containing 7	14						mitochondrion (GO:0005739)				upper_aerodigestive_tract(1)	1		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTAAAACACTGCACAGGACCA	0.403													G|||	72	0.014377	0.0	0.0202	5008	,	,		16607	0.0		0.0457	False		,,,				2504	0.0123				p.L14L		Atlas-SNP	.											.	LYRM7	7	.	0			c.G42A						PASS	.	G		36,4370	41.6+/-74.8	1,34,2168	120.0	116.0	117.0		42	4.3	1.0	5	dbSNP_132	117	374,8226	123.2+/-182.1	12,350,3938	no	coding-synonymous	LYRM7	NM_181705.2		13,384,6106	AA,AG,GG		4.3488,0.8171,3.1524		14/105	130515811	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	90624	exon2			AACACTGCACAGG	BC047079	CCDS4148.1	5q31.1	2013-05-24	2012-10-23	2006-10-17	ENSG00000186687	ENSG00000186687		"""LYR motif containing"""	28072	protein-coding gene	gene with protein product		615831	"""chromosome 5 open reading frame 31"", ""Lyrm7 homolog (mouse)"""	C5orf31		23168492	Standard	NM_181705		Approved	FLJ20796, MZM1L	uc003kvg.1	Q5U5X0	OTTHUMG00000128994	ENST00000379380.4:c.42G>A	5.37:g.130515811G>A		54.0	0.0	0		48.0	23.0	0.479167	NM_181705	A8MPQ9|Q86Y68	Silent	SNP	ENST00000379380.4	37	CCDS4148.1																																																																																			A|0.027;C|0.000;G|0.973	0.027	strong		0.403	LYRM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250983.1	NM_181705	
OR7A10	390892	hgsc.bcm.edu	37	19	14952301	14952301	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:14952301A>C	ENST00000248058.1	-	1	388	c.389T>G	c.(388-390)cTg>cGg	p.L130R		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	130						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					CATGTAGTGCAGAGGGTGACA	0.463																																					p.L130R		Atlas-SNP	.											.	OR7A10	33	.	0			c.T389G						PASS	.						88.0	80.0	82.0					19																	14952301		2203	4300	6503	SO:0001583	missense	390892	exon1			TAGTGCAGAGGGT		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.389T>G	19.37:g.14952301A>C	ENSP00000248058:p.Leu130Arg	88.0	0.0	0		100.0	49.0	0.49	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	a	12.67	2.008986	0.35415	.	.	ENSG00000127515	ENST00000248058	T	0.01516	4.81	2.8	2.8	0.32819	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31747	U	0.007131	T	0.15912	0.0383	H	0.97983	4.12	0.30328	N	0.786887	D	0.89917	1.0	D	0.80764	0.994	T	0.18745	-1.0327	10	0.87932	D	0	.	9.1033	0.36683	1.0:0.0:0.0:0.0	.	130	O76100	OR7AA_HUMAN	R	130	ENSP00000248058:L130R	ENSP00000248058:L130R	L	-	2	0	OR7A10	14813301	1.000000	0.71417	0.951000	0.38953	0.026000	0.11368	7.589000	0.82641	1.306000	0.44926	0.163000	0.16589	CTG	.	.	none		0.463	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
LOXHD1	125336	hgsc.bcm.edu	37	18	44065109	44065109	+	Missense_Mutation	SNP	C	C	T	rs373848470		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44065109C>T	ENST00000398722.4	-	32	5220	c.5221G>A	c.(5221-5223)Gag>Aag	p.E1741K	LOXHD1_ENST00000579038.1_Missense_Mutation_p.E812K|LOXHD1_ENST00000398686.4_Missense_Mutation_p.E258K|LOXHD1_ENST00000300591.6_Missense_Mutation_p.E908K|LOXHD1_ENST00000398705.2_Missense_Mutation_p.E258K|LOXHD1_ENST00000582408.1_Missense_Mutation_p.E846K|LOXHD1_ENST00000536736.1_Missense_Mutation_p.E1957K|LOXHD1_ENST00000441551.2_Missense_Mutation_p.E1813K|LOXHD1_ENST00000441893.2_Missense_Mutation_p.E890K			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1741	PLAT 13. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						ATGACGATCTCGTAGGCTGTA	0.577																																					p.E1957K		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G5869A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,1384		0,0,692	67.0	58.0	61.0		2722,772,772,5869	5.6	1.0	18		61	1,3181		0,1,1590	no	missense,missense,missense,missense	LOXHD1	NM_001145472.2,NM_001145473.2,NM_001173129.1,NM_144612.6	56,56,56,56	0,1,2282	TT,TC,CC		0.0314,0.0,0.0219	probably-damaging,probably-damaging,probably-damaging,probably-damaging	908/1115,258/513,258/458,1957/2212	44065109	1,4565	692	1591	2283	SO:0001583	missense	125336	exon38			CGATCTCGTAGGC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.5221G>A	18.37:g.44065109C>T	ENSP00000381707:p.Glu1741Lys	58.0	0.0	0		60.0	30.0	0.5	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		.	.	.	.	.	.	.	.	.	.	C	18.83	3.707609	0.68615	0.0	3.14E-4	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000398705;ENST00000536736;ENST00000441893;ENST00000398686	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.6	5.6	0.85130	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	.	.	.	.	T	0.71702	0.3371	L	0.45137	1.4	0.58432	D	0.999992	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.81914	0.994;0.991;0.995	T	0.62163	-0.6912	9	0.09338	T	0.73	.	19.9855	0.97347	0.0:1.0:0.0:0.0	.	1957;890;1741	F5GZB4;F8WA52;Q8IVV2	.;.;LOXH1_HUMAN	K	908;1741;258;1957;890;258	ENSP00000300591:E908K;ENSP00000381707:E1741K;ENSP00000381692:E258K;ENSP00000444586:E1957K;ENSP00000409062:E890K;ENSP00000381676:E258K	ENSP00000300591:E908K	E	-	1	0	LOXHD1	42319107	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.974000	0.76122	2.806000	0.96561	0.655000	0.94253	GAG	.	.	weak		0.577	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
SERBP1	26135	hgsc.bcm.edu	37	1	67895779	67895779	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67895779G>A	ENST00000370995.2	-	1	290	c.205C>T	c.(205-207)Cag>Tag	p.Q69*	SERBP1_ENST00000361219.6_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000370990.5_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000370994.4_Nonsense_Mutation_p.Q69*			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	69					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						TTGCGCAGCTGTTTGCCTGCC	0.657																																					p.Q69X		Atlas-SNP	.											.	SERBP1	31	.	0			c.C205T						PASS	.						37.0	46.0	43.0					1																	67895779		2197	4289	6486	SO:0001587	stop_gained	26135	exon1			GCAGCTGTTTGCC	AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.205C>T	1.37:g.67895779G>A	ENSP00000360034:p.Gln69*	127.0	0.0	0		110.0	39.0	0.354545	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Nonsense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	G	38	7.040941	0.98021	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	4.99	4.99	0.66335	.	0.056967	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-3.4359	17.4097	0.87482	0.0:0.0:1.0:0.0	.	.	.	.	X	69	.	ENSP00000354591:Q69X	Q	-	1	0	SERBP1	67668367	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.730000	0.91510	2.471000	0.83476	0.462000	0.41574	CAG	.	.	none		0.657	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067	
COL9A3	1299	hgsc.bcm.edu	37	20	61452556	61452556	+	Silent	SNP	G	G	A	rs149690829	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61452556G>A	ENST00000343916.3	+	6	336	c.333G>A	c.(331-333)ccG>ccA	p.P111P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	111	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					CCCCGGGGCCGCCCGGGCTGG	0.617													G|||	2	0.000399361	0.0	0.0	5008	,	,		16029	0.001		0.0	False		,,,				2504	0.001				p.P111P		Atlas-SNP	.											.	COL9A3	70	.	0			c.G333A						PASS	.	G		0,4396		0,0,2198	40.0	47.0	45.0		333	-9.7	0.0	20	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL9A3	NM_001853.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		111/685	61452556	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	1299	exon6			GGGGCCGCCCGGG	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.333G>A	20.37:g.61452556G>A		61.0	0.0	0		51.0	27.0	0.529412	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			G|1.000;A|0.000	0.000	strong		0.617	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33614391	33614391	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:33614391A>T	ENST00000504830.1	-	16	2814	c.2479T>A	c.(2479-2481)Ttc>Atc	p.F827I	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.F742I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	827	Spacer 1.|TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TACTGCCAGAAGTACATCTGC	0.502										HNSCC(64;0.19)																											p.F827I		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.T2479A						PASS	.						209.0	147.0	168.0					5																	33614391		2203	4300	6503	SO:0001583	missense	81792	exon16			GCCAGAAGTACAT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2479T>A	5.37:g.33614391A>T	ENSP00000422554:p.Phe827Ile	111.0	0.0	0		104.0	10.0	0.0961538	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.940819	0.34283	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.60424	0.19;0.19	5.73	5.73	0.89815	.	0.413754	0.28927	N	0.013686	T	0.59865	0.2225	L	0.34521	1.04	0.80722	D	1	D;B	0.67145	0.996;0.077	P;B	0.62184	0.899;0.052	T	0.55328	-0.8158	10	0.20519	T	0.43	.	10.865	0.46849	0.8593:0.0:0.0:0.1407	.	742;827	P58397-3;P58397	.;ATS12_HUMAN	I	827;742	ENSP00000422554:F827I;ENSP00000344847:F742I	ENSP00000344847:F742I	F	-	1	0	ADAMTS12	33650148	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.846000	0.48262	2.179000	0.69175	0.459000	0.35465	TTC	.	.	none		0.502	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
CACNA1C	775	hgsc.bcm.edu	37	12	2224449	2224449	+	Missense_Mutation	SNP	G	G	A	rs34534613	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:2224449G>A	ENST00000347598.4	+	2	109	c.109G>A	c.(109-111)Ggg>Agg	p.G37R	CACNA1C_ENST00000399641.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G37R|CACNA1C_ENST00000399644.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000480911.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G37R|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G37R	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	37					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGCGGCAGCGGGGCTGGCCCC	0.627													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16109	0.0		0.0	False		,,,				2504	0.001				p.G37R		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G109A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	2,3864		0,2,1931	9.0	11.0	10.0		109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109	5.8	0.8	12	dbSNP_126	10	26,8160		0,26,4067	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125	0,28,5998	AA,AG,GG		0.3176,0.0517,0.2323	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	37/2139,37/2187,37/2180,37/2174,37/2167,37/2159,37/2158,37/2158,37/2158,37/2156,37/2147,37/2147,37/2145,37/2139,37/2139,37/2139,37/2139,37/2136,37/2128,37/2139,37/2174,37/2199,37/2222	2224449	28,12024	1933	4093	6026	SO:0001583	missense	775	exon2			GCAGCGGGGCTGG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.109G>A	12.37:g.2224449G>A	ENSP00000266376:p.Gly37Arg	34.0	0.0	0		34.0	17.0	0.5	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085219	0.76642	5.17E-4	0.003176	ENSG00000151067	ENST00000543114;ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96011	-3.84;-3.82;-3.85;-3.87;-3.82;-3.81;-3.83;-3.73;-3.77;-3.88;-3.78;-3.77;-3.88;-3.86;-3.74;-3.66;-3.88;-3.83;-3.81;-3.86;-3.76;-3.85;-3.88	5.77	5.77	0.91146	.	0.513281	0.18641	N	0.135284	D	0.97025	0.9028	L	0.48642	1.525	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.999;0.999;1.0;0.999;0.999;0.999;0.999;1.0;0.138;0.999;0.998;0.999;0.999;0.999;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;D	0.91635	0.967;0.967;0.949;0.999;0.967;0.967;0.999;0.967;0.967;0.967;0.967;0.999;0.055;0.967;0.914;0.967;0.967;0.967;0.967;0.967	D	0.97376	0.9979	10	0.87932	D	0	.	19.9785	0.97317	0.0:0.0:1.0:0.0	rs34534613	37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	R	67;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37	ENSP00000336982:G37R;ENSP00000382563:G37R;ENSP00000437936:G37R;ENSP00000382552:G37R;ENSP00000382547:G37R;ENSP00000382506:G37R;ENSP00000382530:G37R;ENSP00000382546:G37R;ENSP00000382500:G37R;ENSP00000382549:G37R;ENSP00000266376:G37R;ENSP00000382515:G37R;ENSP00000382510:G37R;ENSP00000341092:G37R;ENSP00000382537:G37R;ENSP00000329877:G37R;ENSP00000382557:G37R;ENSP00000385724:G37R;ENSP00000382512:G37R;ENSP00000382542:G37R;ENSP00000382526:G37R;ENSP00000385896:G37R;ENSP00000382504:G37R	ENSP00000329877:G37R	G	+	1	0	CACNA1C	2094710	1.000000	0.71417	0.779000	0.31741	0.079000	0.17450	9.599000	0.98280	2.729000	0.93468	0.555000	0.69702	GGG	G|0.997;A|0.003	0.003	strong		0.627	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
SLC22A15	55356	hgsc.bcm.edu	37	1	116577849	116577849	+	Missense_Mutation	SNP	C	C	T	rs201564754		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116577849C>T	ENST00000369503.4	+	7	1116	c.986C>T	c.(985-987)gCg>gTg	p.A329V	SLC22A15_ENST00000481127.1_3'UTR	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	329					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		ACTCTGAGTGCGGGTGATCTA	0.453													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18324	0.0		0.0	False		,,,				2504	0.0				p.A329V		Atlas-SNP	.											.	SLC22A15	65	.	0			c.C986T						PASS	.						190.0	180.0	183.0					1																	116577849		1941	4155	6096	SO:0001583	missense	55356	exon7			TGAGTGCGGGTGA	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"""Solute carriers"""	20301	protein-coding gene	gene with protein product		608275	"""solute carrier family 22 (organic cation transporter), member 15"""			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.986C>T	1.37:g.116577849C>T	ENSP00000358515:p.Ala329Val	245.0	0.0	0		247.0	64.0	0.259109	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	37	CCDS44198.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	18.02	3.529828	0.64860	.	.	ENSG00000163393	ENST00000369503	T	0.59083	0.29	5.76	5.76	0.90799	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.109676	0.64402	D	0.000009	T	0.21267	0.0512	N	0.25890	0.77	0.80722	D	1	B	0.16166	0.016	B	0.21360	0.034	T	0.07158	-1.0787	10	0.02654	T	1	.	10.9622	0.47391	0.0:0.8876:0.0:0.1124	.	329	Q8IZD6	S22AF_HUMAN	V	329	ENSP00000358515:A329V	ENSP00000358515:A329V	A	+	2	0	SLC22A15	116379372	0.992000	0.36948	1.000000	0.80357	0.995000	0.86356	2.889000	0.48601	2.722000	0.93159	0.650000	0.86243	GCG	C|1.000;T|0.000	0.000	strong		0.453	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
DIP2A	23181	hgsc.bcm.edu	37	21	47971585	47971585	+	Missense_Mutation	SNP	G	G	T	rs574049766		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47971585G>T	ENST00000417564.2	+	24	2899	c.2878G>T	c.(2878-2880)Gct>Tct	p.A960S	DIP2A_ENST00000318711.7_Missense_Mutation_p.A961S|DIP2A_ENST00000400274.1_Missense_Mutation_p.A956S|DIP2A_ENST00000427143.2_Missense_Mutation_p.A896S			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	960					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAACCTGGTTGCTGGGAAGAG	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		17861	0.0		0.001	False		,,,				2504	0.0				p.A960S		Atlas-SNP	.											.	DIP2A	332	.	0			c.G2878T						PASS	.						34.0	36.0	36.0					21																	47971585		1996	4193	6189	SO:0001583	missense	23181	exon24			CTGGTTGCTGGGA	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2878G>T	21.37:g.47971585G>T	ENSP00000392066:p.Ala960Ser	66.0	0.0	0		95.0	32.0	0.336842	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.819361	0.32145	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000417564	T;T;T;T	0.22945	1.94;1.94;1.94;1.93	5.34	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	L	0.42245	1.32	0.58432	D	0.999999	B;B;B	0.27117	0.132;0.038;0.168	B;B;B	0.31191	0.081;0.013;0.125	T	0.04268	-1.0964	10	0.02654	T	1	-11.1468	13.3584	0.60642	0.0:0.0:0.7124:0.2876	.	961;896;960	E9PER1;E7EMA5;Q14689	.;.;DIP2A_HUMAN	S	956;896;961;960	ENSP00000383133:A956S;ENSP00000400528:A896S;ENSP00000323633:A961S;ENSP00000392066:A960S	ENSP00000323633:A961S	A	+	1	0	DIP2A	46796013	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	3.230000	0.51286	0.565000	0.29255	0.655000	0.94253	GCT	.	.	none		0.562	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
KIF1A	547	hgsc.bcm.edu	37	2	241710437	241710437	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:241710437T>C	ENST00000320389.7	-	14	1423	c.1265A>G	c.(1264-1266)gAg>gGg	p.E422G	KIF1A_ENST00000498729.2_Missense_Mutation_p.E431G	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	422					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CAAGATGCGCTCGTGGAGGCT	0.647																																					p.E431G		Atlas-SNP	.											.	KIF1A	152	.	0			c.A1292G						PASS	.						44.0	56.0	52.0					2																	241710437		2080	4234	6314	SO:0001583	missense	547	exon15			ATGCGCTCGTGGA	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.1265A>G	2.37:g.241710437T>C	ENSP00000322791:p.Glu422Gly	45.0	0.0	0		63.0	15.0	0.238095	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641091	0.67244	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.73897	-0.66;-0.72;-0.79	4.11	4.11	0.48088	.	0.122605	0.53938	N	0.000052	T	0.60274	0.2256	L	0.27053	0.805	0.58432	D	0.999997	B;P;P	0.40909	0.002;0.688;0.732	B;B;B	0.37601	0.008;0.235;0.254	T	0.59768	-0.7392	10	0.29301	T	0.29	.	13.1308	0.59380	0.0:0.0:0.0:1.0	.	431;431;422	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	G	422;431;431;431	ENSP00000322791:E422G;ENSP00000438388:E431G;ENSP00000384231:E431G	ENSP00000322791:E422G	E	-	2	0	KIF1A	241359110	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.804000	0.85993	1.508000	0.48769	0.454000	0.30748	GAG	.	.	none		0.647	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
SPATC1	375686	hgsc.bcm.edu	37	8	145095768	145095768	+	Missense_Mutation	SNP	C	C	T	rs150277218	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145095768C>T	ENST00000377470.3	+	3	1168	c.1066C>T	c.(1066-1068)Cac>Tac	p.H356Y	SPATC1_ENST00000447830.2_Missense_Mutation_p.H356Y	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	356						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AAGCACCACCCACATCGCCCA	0.677																																					p.H356Y		Atlas-SNP	.											.	SPATC1	77	.	0			c.C1066T						PASS	.	C	TYR/HIS,TYR/HIS	3,4391		0,3,2194	150.0	53.0	86.0		1066,1066	2.0	0.1	8	dbSNP_134	86	1,8593		0,1,4296	yes	missense,missense	SPATC1	NM_001134374.1,NM_198572.2	83,83	0,4,6490	TT,TC,CC		0.0116,0.0683,0.0308	possibly-damaging,possibly-damaging	356/442,356/592	145095768	4,12984	2197	4297	6494	SO:0001583	missense	375686	exon3			ACCACCCACATCG	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.1066C>T	8.37:g.145095768C>T	ENSP00000366690:p.His356Tyr	58.0	0.0	0		64.0	30.0	0.46875	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	ENST00000377470.3	37	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	C	10.60	1.395949	0.25205	6.83E-4	1.16E-4	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.49139	0.79	3.94	1.99	0.26369	.	.	.	.	.	T	0.45135	0.1327	L	0.51422	1.61	0.09310	N	1	D;D	0.61697	0.99;0.99	P;P	0.57324	0.818;0.818	T	0.39165	-0.9627	9	0.02654	T	1	.	4.0862	0.09948	0.2339:0.6394:0.0:0.1267	.	356;356	B4DWW9;Q76KD6	.;SPERI_HUMAN	Y	356	ENSP00000366690:H356Y	ENSP00000366690:H356Y	H	+	1	0	SPATC1	145167756	0.001000	0.12720	0.051000	0.19133	0.200000	0.23975	0.160000	0.16462	0.717000	0.32145	0.561000	0.74099	CAC	C|0.999;T|0.001	0.001	strong		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572	
CXorf58	254158	hgsc.bcm.edu	37	X	23933912	23933912	+	Splice_Site	SNP	G	G	A	rs62584865	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:23933912G>A	ENST00000379211.3	+	4	860		c.e4+1			NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						TTAGATTCAGGTAATGTATCT	0.308													G|||	15	0.00397351	0.0	0.0029	3775	,	,		14821	0.0		0.006	False		,,,				2504	0.0072				.		Atlas-SNP	.											.	CXorf58	53	.	0			c.311+1G>A						PASS	.	G	,	9,3825		0,5,4,1627,566	51.0	43.0	46.0		,	5.8	1.0	X	dbSNP_129	46	128,6599		0,98,30,2330,1841	yes	splice-5,splice-5	CXorf58	NM_001169574.1,NM_152761.2	,	0,103,34,3957,2407	AA,AG,A,GG,G		1.9028,0.2347,1.2972	,	,	23933912	137,10424	2202	4299	6501	SO:0001630	splice_region_variant	254158	exon4			ATTCAGGTAATGT	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.311+1G>A	X.37:g.23933912G>A		77.0	0.0	0		110.0	40.0	0.363636	NM_001169574		Splice_Site	SNP	ENST00000379211.3	37	CCDS14209.1	6	0.003616636528028933	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005291005291005291	g	13.92	2.380686	0.42207	0.002347	0.019028	ENSG00000165182	ENST00000379211;ENST00000435707	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8642	0.79052	0.0:0.0:1.0:0.0	rs62584865	.	.	.	.	-1	.	.	.	+	.	.	CXorf58	23843833	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	5.194000	0.65125	2.460000	0.83146	0.540000	0.68198	.	G|0.991;A|0.009	0.009	strong		0.308	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	Intron
RANBP17	64901	hgsc.bcm.edu	37	5	170338066	170338066	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:170338066T>G	ENST00000523189.1	+	7	852	c.688T>G	c.(688-690)Ttc>Gtc	p.F230V		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	230					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TAACTTTGACTTCATTGGCAG	0.403			T	TRD@	ALL																																p.F230V		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T688G						PASS	.						87.0	81.0	83.0					5																	170338066		2203	4298	6501	SO:0001583	missense	64901	exon7			TTTGACTTCATTG	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.688T>G	5.37:g.170338066T>G	ENSP00000427975:p.Phe230Val	143.0	0.0	0		171.0	41.0	0.239766	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	29.1|29.1	4.975804|4.975804	0.92982|0.92982	.|.	.|.	ENSG00000204764|ENSG00000204764	ENST00000523189;ENST00000545246|ENST00000522734	T|.	0.68025|.	-0.3|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Armadillo-type fold (1);|.	0.000000|.	0.64402|.	D|.	0.000008|.	D|D	0.85366|0.85366	0.5680|0.5680	M|M	0.93106|0.93106	3.38|3.38	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.71674|.	0.998|.	D|.	0.69307|.	0.963|.	D|D	0.89121|0.89121	0.3503|0.3503	10|5	0.87932|.	D|.	0|.	-18.1852|-18.1852	15.4379|15.4379	0.75160|0.75160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	230|.	Q9H2T7|.	RBP17_HUMAN|.	V|R	230;126|12	ENSP00000427975:F230V|.	ENSP00000373770:F230V|.	F|L	+|+	1|2	0|0	RANBP17|RANBP17	170270644|170270644	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.898000|7.898000	0.87363|0.87363	2.174000|2.174000	0.68829|0.68829	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.	none		0.403	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
PRRC2A	7916	hgsc.bcm.edu	37	6	31603046	31603046	+	Silent	SNP	C	C	T	rs139053368	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31603046C>T	ENST00000376033.2	+	22	5532	c.5298C>T	c.(5296-5298)gaC>gaT	p.D1766D	PRRC2A_ENST00000376007.4_Silent_p.D1766D	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1766	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GCACTAGTGACAAGGTCTGTG	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		19020	0.0		0.0	False		,,,				2504	0.002				p.D1766D		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C5298T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	86.0	77.0	80.0		5298,5298	3.8	1.0	6	dbSNP_134	80	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	,	1766/2158,1766/2158	31603046	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	7916	exon22			TAGTGACAAGGTC	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5298C>T	6.37:g.31603046C>T		114.0	0.0	0		105.0	19.0	0.180952	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			C|0.999;T|0.001	0.001	strong		0.567	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
COL8A1	1295	hgsc.bcm.edu	37	3	99513830	99513830	+	Missense_Mutation	SNP	G	G	A	rs139380413		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:99513830G>A	ENST00000261037.3	+	5	1465	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	COL8A1_ENST00000273342.4_Missense_Mutation_p.R362Q	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	362	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						AAAGGTGACCGGGGCATGGGA	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		17087	0.0		0.001	False		,,,				2504	0.0				p.R362Q		Atlas-SNP	.											.	COL8A1	68	.	0			c.G1085A						PASS	.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	25.0	31.0	29.0		1085,1085	2.8	1.0	3	dbSNP_134	29	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	COL8A1	NM_020351.2,NM_001850.3	43,43	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign,benign	362/745,362/745	99513830	4,13002	2203	4300	6503	SO:0001583	missense	1295	exon5			GTGACCGGGGCAT	AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"""Collagens"""	2215	protein-coding gene	gene with protein product		120251	"""chromosome 3 open reading frame 7"""	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.1085G>A	3.37:g.99513830G>A	ENSP00000261037:p.Arg362Gln	50.0	0.0	0		39.0	20.0	0.512821	NM_001850	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	37	CCDS2934.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.23	1.577317	0.28092	2.27E-4	3.49E-4	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.90788	-2.73;-2.73	5.93	2.8	0.32819	.	0.294580	0.37669	N	0.001998	D	0.82861	0.5129	L	0.38733	1.17	0.34343	D	0.68898	B;B	0.22541	0.071;0.071	B;B	0.15052	0.012;0.012	T	0.75536	-0.3283	10	0.17832	T	0.49	.	9.3612	0.38197	0.1574:0.0:0.8426:0.0	.	363;362	E7EPK9;P27658	.;CO8A1_HUMAN	Q	362	ENSP00000261037:R362Q;ENSP00000273342:R362Q	ENSP00000261037:R362Q	R	+	2	0	COL8A1	100996520	0.573000	0.26676	0.966000	0.40874	0.962000	0.63368	3.041000	0.49807	0.239000	0.21243	0.563000	0.77884	CGG	G|0.999;A|0.001	0.001	strong		0.627	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850	
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843666	16843666	+	Missense_Mutation	SNP	C	C	T	rs104894649		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:16843666C>T	ENST00000261652.2	-	4	617	c.605G>A	c.(604-606)cGt>cAt	p.R202H	TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.R156H|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.R156H	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	202			R -> H (in CVID2). {ECO:0000269|PubMed:16007086}.		B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						CGGACTTTGACGGGGCCTTGA	0.652									IgA Deficiency, Selective				.|||	1	0.000199681	0.0	0.0	5008	,	,		16946	0.0		0.0	False		,,,				2504	0.001				p.R202H		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.G605A	GRCh37	CM052923	TNFRSF13B	M	rs104894649	PASS	.	C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	93.0	100.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	605	2.0	0.0	17	dbSNP_132	98	7,8593	5.7+/-21.5	0,7,4293	yes	missense	TNFRSF13B	NM_012452.2	29	0,9,6494	TT,TC,CC		0.0814,0.0454,0.0692	benign	202/294	16843666	9,12997	2203	4300	6503	SO:0001583	missense	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	CTTTGACGGGGCC	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.605G>A	17.37:g.16843666C>T	ENSP00000261652:p.Arg202His	46.0	0.0	0		61.0	32.0	0.52459	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	.	.	.	.	.	.	.	.	.	.	c	7.351	0.622884	0.14193	4.54E-4	8.14E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.93488	-3.23;-3.2	3.03	2.01	0.26516	.	0.476795	0.19299	N	0.117685	D	0.83543	0.5277	N	0.19112	0.55	0.09310	A	1.25395e-09	B;P	0.34892	0.3;0.474	B;B	0.25140	0.058;0.043	T	0.82168	-0.0591	9	0.54805	T	0.06	0.0038	6.5787	0.22581	0.0:0.8475:0.0:0.1525	.	156;202	O14836-2;O14836	.;TR13B_HUMAN	H	156;202	ENSP00000413453:R156H;ENSP00000261652:R202H	ENSP00000261652:R202H	R	-	2	0	TNFRSF13B	16784391	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.497000	0.22514	0.552000	0.29026	0.558000	0.71614	CGT	C|0.999;T|0.001	0.001	strong		0.652	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
CUTA	51596	hgsc.bcm.edu	37	6	33384473	33384473	+	Missense_Mutation	SNP	C	C	T	rs41267649	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33384473C>T	ENST00000488034.1	-	6	615	c.494G>A	c.(493-495)cGc>cAc	p.R165H	CUTA_ENST00000607266.1_Missense_Mutation_p.R142H|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000494751.1_Intron|CUTA_ENST00000374500.5_Missense_Mutation_p.R184H|CUTA_ENST00000374496.3_Missense_Mutation_p.R142H|CUTA_ENST00000488478.1_Silent_p.A148A|CUTA_ENST00000440279.3_Missense_Mutation_p.R142H	NM_001014837.1|NM_001014838.1|NM_001014840.1|NM_015921.2	NP_001014837.1|NP_001014838.1|NP_001014840.1|NP_057005.1	O60888	CUTA_HUMAN	cutA divalent cation tolerance homolog (E. coli)	165					protein localization (GO:0008104)|response to metal ion (GO:0010038)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)		SLC22A1/CUTA(2)	kidney(1)|lung(3)|urinary_tract(1)	5						TGTGACCTGGCGCACCCACTG	0.532													C|||	28	0.00559105	0.0008	0.0101	5008	,	,		17858	0.0		0.0189	False		,,,				2504	0.001				p.R184H		Atlas-SNP	.											.	CUTA	5	.	0			c.G551A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	30,4376	36.0+/-67.5	0,30,2173	107.0	91.0	96.0		551,425,425,494,425	-5.2	0.2	6	dbSNP_127	96	191,8409	84.0+/-146.5	3,185,4112	yes	missense,missense,missense,missense,missense	CUTA	NM_001014433.2,NM_001014837.1,NM_001014838.1,NM_001014840.1,NM_015921.2	29,29,29,29,29	3,215,6285	TT,TC,CC		2.2209,0.6809,1.6992	benign,benign,benign,benign,benign	184/199,142/157,142/157,165/180,142/157	33384473	221,12785	2203	4300	6503	SO:0001583	missense	51596	exon6			ACCTGGCGCACCC	AF106943	CCDS4779.1, CCDS34432.1, CCDS34433.1	6p21.32	2008-02-04	2006-02-15	2006-02-15	ENSG00000112514	ENSG00000112514			21101	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 82"", ""acetylcholinesterase-associated protein"""	C6orf82, ACHAP			Standard	XM_006715108		Approved		uc003oen.1	O60888	OTTHUMG00000031254	ENST00000488034.1:c.494G>A	6.37:g.33384473C>T	ENSP00000417544:p.Arg165His	183.0	0.0	0		173.0	142.0	0.820809	NM_001014433	A2AB26|A2BEL4|Q3B784|Q5JXM9|Q5SU05|Q9NYQ9	Missense_Mutation	SNP	ENST00000488034.1	37	CCDS34433.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	7.391	0.630765	0.14322	0.006809	0.022209	ENSG00000112514	ENST00000374500;ENST00000440279;ENST00000488034;ENST00000374496	.	.	.	4.68	-5.17	0.02849	Nitrogen regulatory PII-like, alpha/beta (1);	0.671906	0.15234	N	0.273279	T	0.08980	0.0222	N	0.16130	0.375	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.18777	-1.0326	9	0.38643	T	0.18	-10.3034	13.7621	0.62973	0.0:0.2317:0.0:0.7683	rs41267649	184;165	O60888-2;O60888	.;CUTA_HUMAN	H	184;142;165;142	.	ENSP00000363620:R142H	R	-	2	0	CUTA	33492451	0.003000	0.15002	0.167000	0.22817	0.437000	0.31866	-1.933000	0.01553	-1.162000	0.02797	-0.766000	0.03442	CGC	C|0.986;T|0.014	0.014	strong		0.532	CUTA-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076541.3	NM_015921	
RIN2	54453	hgsc.bcm.edu	37	20	19937289	19937289	+	Silent	SNP	C	C	T	rs368413043		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:19937289C>T	ENST00000255006.6	+	4	485	c.336C>T	c.(334-336)tcC>tcT	p.S112S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Silent_p.S63S	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	63	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						GTGGCTATTCCGAGGAAGAGG	0.567																																					p.S112S		Atlas-SNP	.											.	RIN2	126	.	0			c.C336T						PASS	.	C	,	2,4094		0,2,2046	48.0	52.0	51.0		336,189	-10.5	0.0	20		51	10,8368		0,10,4179	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,12,6225	TT,TC,CC		0.1194,0.0488,0.0962	,	112/945,63/896	19937289	12,12462	2048	4189	6237	SO:0001819	synonymous_variant	54453	exon4			CTATTCCGAGGAA	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.336C>T	20.37:g.19937289C>T		55.0	0.0	0		66.0	33.0	0.5	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			.	.	weak		0.567	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
KCNU1	157855	hgsc.bcm.edu	37	8	36664917	36664917	+	Missense_Mutation	SNP	G	G	A	rs180964986		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:36664917G>A	ENST00000399881.3	+	6	642	c.605G>A	c.(604-606)cGc>cAc	p.R202H		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	202					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R202H(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGAGCCTTGCGCCTGCTAGAA	0.443													G|||	1	0.000199681	0.0	0.0	5008	,	,		17222	0.001		0.0	False		,,,				2504	0.0				p.R202H		Atlas-SNP	.											KCNU1,NS,carcinoma,0,1	KCNU1	359	1	2	Substitution - Missense(2)	endometrium(2)	c.G605A						PASS	.						145.0	144.0	144.0					8																	36664917		1860	4104	5964	SO:0001583	missense	157855	exon6			CCTTGCGCCTGCT	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.605G>A	8.37:g.36664917G>A	ENSP00000382770:p.Arg202His	100.0	0.0	0		73.0	18.0	0.246575	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.97	3.268650	0.59540	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	D;D	0.99591	-6.24;-6.24	5.22	3.37	0.38596	Ion transport (1);	0.000000	0.34555	U	0.003866	D	0.99333	0.9766	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.99320	1.0906	10	0.87932	D	0	-0.2079	8.4945	0.33119	0.0852:0.153:0.7618:0.0	.	202	A8MYU2	KCNU1_HUMAN	H	202	ENSP00000429951:R202H;ENSP00000382770:R202H	ENSP00000382770:R202H	R	+	2	0	KCNU1	36784075	0.998000	0.40836	0.285000	0.24819	0.224000	0.24922	4.805000	0.62561	1.174000	0.42811	0.650000	0.86243	CGC	G|1.000;A|0.000	0.000	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
UBR2	23304	hgsc.bcm.edu	37	6	42613298	42613298	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42613298T>C	ENST00000372899.1	+	21	2637	c.2379T>C	c.(2377-2379)caT>caC	p.H793H	UBR2_ENST00000372883.3_Silent_p.H297H|UBR2_ENST00000372901.1_Silent_p.H793H	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	793					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CTATGGCTCATAGTGAATTGG	0.378																																					p.H793H		Atlas-SNP	.											.	UBR2	134	.	0			c.T2379C						PASS	.						114.0	109.0	111.0					6																	42613298		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon21			GGCTCATAGTGAA	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2379T>C	6.37:g.42613298T>C		45.0	0.0	0		47.0	20.0	0.425532	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			.	.	none		0.378	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ATAD2	29028	hgsc.bcm.edu	37	8	124357253	124357253	+	Silent	SNP	G	G	A	rs16898247	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124357253G>A	ENST00000287394.5	-	19	2696	c.2589C>T	c.(2587-2589)caC>caT	p.H863H	RNU6-875P_ENST00000516488.1_RNA|ATAD2_ENST00000521903.1_Silent_p.H181H	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	863					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CCCACCACACGTGGATATGAG	0.398													G|||	741	0.147963	0.5053	0.0663	5008	,	,		16240	0.001		0.0189	False		,,,				2504	0.0072				p.H863H		Atlas-SNP	.											ATAD2,NS,carcinoma,-2,1	ATAD2	160	1	0			c.C2589T						PASS	.	G		1923,2483	548.7+/-377.6	424,1075,704	236.0	207.0	216.0		2589	2.7	1.0	8	dbSNP_123	216	186,8414	82.6+/-145.2	2,182,4116	no	coding-synonymous	ATAD2	NM_014109.3		426,1257,4820	AA,AG,GG		2.1628,43.645,16.2156		863/1391	124357253	2109,10897	2203	4300	6503	SO:0001819	synonymous_variant	29028	exon19			CCACACGTGGATA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.2589C>T	8.37:g.124357253G>A		69.0	0.0	0		91.0	40.0	0.43956	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																			G|0.843;A|0.157	0.157	strong		0.398	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
ZBTB24	9841	hgsc.bcm.edu	37	6	109796673	109796673	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:109796673G>A	ENST00000230122.3	-	5	1384	c.1217C>T	c.(1216-1218)cCg>cTg	p.P406L		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	406					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		TTTGCATTCCGGTAATGAGTG	0.448																																					p.P406L		Atlas-SNP	.											.	ZBTB24	64	.	0			c.C1217T						PASS	.						184.0	153.0	163.0					6																	109796673		2203	4300	6503	SO:0001583	missense	9841	exon5			CATTCCGGTAATG	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	21143	protein-coding gene	gene with protein product	"""POZ (BTB) and AT hook containing zinc finger 2"""	614064	"""zinc finger protein 450"""	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1217C>T	6.37:g.109796673G>A	ENSP00000230122:p.Pro406Leu	82.0	0.0	0		74.0	4.0	0.0540541	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.412005	0.62511	.	.	ENSG00000112365	ENST00000230122	T	0.35605	1.3	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.26557	0.0649	N	0.01493	-0.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54879	-0.8227	10	0.36615	T	0.2	-25.2969	20.8794	0.99867	0.0:0.0:1.0:0.0	.	406	O43167	ZBT24_HUMAN	L	406	ENSP00000230122:P406L	ENSP00000230122:P406L	P	-	2	0	ZBTB24	109903366	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.334000	0.79224	2.941000	0.99782	0.655000	0.94253	CCG	.	.	none		0.448	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:196825256G>C	ENST00000312428.6	-	18	2719	c.2619C>G	c.(2617-2619)gtC>gtG	p.V873V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	873	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AAAAAGAGGAGACTGTGGAGT	0.448													G|||	94	0.01877	0.0045	0.0389	5008	,	,		19851	0.0		0.0507	False		,,,				2504	0.0102				p.V873V		Atlas-SNP	.											.	DNAH7	512	.	0			c.C2619G						PASS	.	G		30,3736		0,30,1853	105.0	103.0	104.0		2619	2.4	0.8	2	dbSNP_132	104	347,7895		8,331,3782	no	coding-synonymous	DNAH7	NM_018897.2		8,361,5635	CC,CG,GG		4.2101,0.7966,3.1396		873/4025	196825256	377,11631	1883	4121	6004	SO:0001819	synonymous_variant	56171	exon18			AGAGGAGACTGTG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2619C>G	2.37:g.196825256G>C		106.0	0.0	0		128.0	80.0	0.625	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.969;C|0.031	0.031	strong		0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
VIL1	7429	hgsc.bcm.edu	37	2	219313993	219313993	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219313993A>C	ENST00000248444.5	+	20	2506	c.2418A>C	c.(2416-2418)ccA>ccC	p.P806P	VIL1_ENST00000392114.2_Silent_p.P495P	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	806	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.|Headpiece.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGATGACTCCAGCTGCCTTCT	0.478																																					p.P806P		Atlas-SNP	.											.	VIL1	65	.	0			c.A2418C						PASS	.						229.0	230.0	230.0					2																	219313993		2203	4300	6503	SO:0001819	synonymous_variant	7429	exon20			GACTCCAGCTGCC	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.2418A>C	2.37:g.219313993A>C		119.0	0.0	0		101.0	48.0	0.475248	NM_007127	B2R9A7|Q53S11|Q96AC8	Silent	SNP	ENST00000248444.5	37	CCDS2417.1																																																																																			.	.	none		0.478	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127	
EPPK1	83481	hgsc.bcm.edu	37	8	144943223	144943223	+	Missense_Mutation	SNP	T	T	C	rs139952490	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144943223T>C	ENST00000525985.1	-	2	4270	c.4199A>G	c.(4198-4200)aAc>aGc	p.N1400S				P58107	EPIPL_HUMAN	epiplakin 1	1400						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GAAGAACTTGTTGTCCTTGTC	0.627													T|||	41	0.0081869	0.0272	0.0043	5008	,	,		21219	0.0		0.002	False		,,,				2504	0.0				p.N1400S		Atlas-SNP	.											.	EPPK1	199	.	0			c.A4199G						PASS	.	T	SER/ASN	50,4324		0,50,2137	29.0	34.0	32.0		4199	0.7	0.0	8	dbSNP_134	32	8,8560		0,8,4276	yes	missense	EPPK1	NM_031308.1	46	0,58,6413	CC,CT,TT		0.0934,1.1431,0.4482	benign	1400/2420	144943223	58,12884	2187	4284	6471	SO:0001583	missense	83481	exon1			AACTTGTTGTCCT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4199A>G	8.37:g.144943223T>C	ENSP00000436337:p.Asn1400Ser	36.0	0.0	0		50.0	20.0	0.4	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		11	0.005036630036630037	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	9.127	1.010504	0.19277	0.011431	9.34E-4	ENSG00000227184	ENST00000525985	T	0.66280	-0.2	4.66	0.728	0.18260	.	.	.	.	.	T	0.15955	0.0384	N	0.08118	0	0.20764	N	0.999852	B	0.12013	0.005	B	0.04013	0.001	T	0.12682	-1.0538	9	0.07175	T	0.84	.	0.4678	0.00527	0.2139:0.3149:0.1697:0.3015	.	1400	E9PPU0	.	S	1400	ENSP00000436337:N1400S	ENSP00000436337:N1400S	N	-	2	0	EPPK1	145015211	0.000000	0.05858	0.008000	0.14137	0.598000	0.36846	-0.047000	0.11963	0.046000	0.15833	0.533000	0.62120	AAC	T|0.995;C|0.005	0.005	strong		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ACVR1C	130399	hgsc.bcm.edu	37	2	158412701	158412701	+	Missense_Mutation	SNP	T	T	G	rs55920843	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:158412701T>G	ENST00000243349.8	-	3	808	c.448A>C	c.(448-450)Aat>Cat	p.N150H	ACVR1C_ENST00000335450.7_Intron|ACVR1C_ENST00000409680.3_Missense_Mutation_p.N100H|ACVR1C_ENST00000348328.5_Intron	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						TCCTCCACATTTGGTCTCTTT	0.478													T|||	18	0.00359425	0.0008	0.0	5008	,	,		16524	0.001		0.0149	False		,,,				2504	0.001				p.N150H		Atlas-SNP	.											.	ACVR1C	85	.	0			c.A448C						PASS	.	T	HIS/ASN,,,HIS/ASN	12,4394	19.1+/-41.9	0,12,2191	101.0	89.0	93.0		298,,,448	5.7	0.3	2	dbSNP_129	93	92,8508	51.9+/-112.3	0,92,4208	yes	missense,intron,intron,missense	ACVR1C	NM_001111031.1,NM_001111032.1,NM_001111033.1,NM_145259.2	68,,,68	0,104,6399	GG,GT,TT		1.0698,0.2724,0.7996	benign,,,benign	100/444,,,150/494	158412701	104,12902	2203	4300	6503	SO:0001583	missense	130399	exon3			CCACATTTGGTCT	BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.448A>C	2.37:g.158412701T>G	ENSP00000243349:p.Asn150His	146.0	0.0	0		134.0	33.0	0.246269	NM_145259		Missense_Mutation	SNP	ENST00000243349.8	37	CCDS2205.1	13	0.005952380952380952	0	0.0	0	0.0	1	0.0017482517482517483	12	0.0158311345646438	T	11.40	1.627039	0.28978	0.002724	0.010698	ENSG00000123612	ENST00000243349;ENST00000409680	D;D	0.88124	-2.34;-2.24	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000021	T	0.71829	0.3386	L	0.55481	1.735	0.80722	D	1	B	0.10296	0.003	B	0.15870	0.014	T	0.72384	-0.4310	10	0.16420	T	0.52	.	10.8735	0.46899	0.1405:0.0:0.0:0.8595	rs55920843	150	Q8NER5	ACV1C_HUMAN	H	150;100	ENSP00000243349:N150H;ENSP00000387168:N100H	ENSP00000243349:N150H	N	-	1	0	ACVR1C	158120947	0.422000	0.25473	0.256000	0.24389	0.757000	0.42996	2.177000	0.42509	2.189000	0.69895	0.528000	0.53228	AAT	T|0.993;G|0.007	0.007	strong		0.478	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259	
SNX5	27131	hgsc.bcm.edu	37	20	17933265	17933265	+	Missense_Mutation	SNP	C	C	T	rs145056868		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17933265C>T	ENST00000377768.3	-	6	791	c.479G>A	c.(478-480)cGc>cAc	p.R160H	SNX5_ENST00000377759.4_Missense_Mutation_p.R160H|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	160	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						ATGAAAGTTGCGATCTTTACT	0.368													C|||	1	0.000199681	0.0	0.0	5008	,	,		21023	0.0		0.001	False		,,,				2504	0.0				p.R160H		Atlas-SNP	.											.	SNX5	38	.	0			c.G479A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	73.0	69.0	71.0		479,479	5.7	1.0	20	dbSNP_134	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	SNX5	NM_014426.2,NM_152227.1	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	160/405,160/405	17933265	2,13004	2203	4300	6503	SO:0001583	missense	27131	exon5			AAGTTGCGATCTT	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.479G>A	20.37:g.17933265C>T	ENSP00000366998:p.Arg160His	77.0	0.0	0		55.0	30.0	0.545455	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	5.968	0.362556	0.11296	0.0	2.33E-4	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277;ENST00000419004	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.66	5.66	0.87406	Phox homologous domain (5);	0.254317	0.45361	D	0.000366	T	0.15565	0.0375	N	0.03154	-0.405	0.41418	D	0.987781	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.18935	-1.0321	10	0.21540	T	0.41	.	8.5702	0.33565	0.0:0.7445:0.1402:0.1153	.	181;160	B7Z476;Q9Y5X3	.;SNX5_HUMAN	H	160;160;123;125	ENSP00000366998:R160H;ENSP00000366988:R160H;ENSP00000404448:R123H;ENSP00000406731:R125H	ENSP00000366988:R160H	R	-	2	0	SNX5	17881265	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.153000	0.42282	2.831000	0.97527	0.650000	0.86243	CGC	C|1.000;T|0.000	0.000	strong		0.368	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
SLC4A5	57835	hgsc.bcm.edu	37	2	74450058	74450058	+	Missense_Mutation	SNP	C	C	T	rs36081793	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:74450058C>T	ENST00000377634.4	-	30	3715	c.3316G>A	c.(3316-3318)Gtt>Att	p.V1106I	SLC4A5_ENST00000358683.4_Missense_Mutation_p.V988I|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000423644.1_3'UTR|SLC4A5_ENST00000346834.4_Missense_Mutation_p.V1009I|SLC4A5_ENST00000359484.4_Missense_Mutation_p.V988I|SLC4A5_ENST00000394019.2_Missense_Mutation_p.V1090I|SLC4A5_ENST00000377632.1_Missense_Mutation_p.V1009I|SLC4A5_ENST00000357822.5_Missense_Mutation_p.V1106I|RP11-287D1.3_ENST00000451608.2_3'UTR					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ATCTTTATAACCGAGGGAGGA	0.418													C|||	61	0.0121805	0.0023	0.0288	5008	,	,		20198	0.0		0.0308	False		,,,				2504	0.0072				p.V1106I		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G3316A						PASS	.	C	ILE/VAL,ILE/VAL	33,4373	39.2+/-71.8	1,31,2171	121.0	119.0	120.0		3316,3268	5.1	1.0	2	dbSNP_126	120	291,8309	107.0+/-167.8	4,283,4013	yes	missense,missense	SLC4A5	NM_021196.3,NM_133478.2	29,29	5,314,6184	TT,TC,CC		3.3837,0.749,2.4912	possibly-damaging,possibly-damaging	1106/1138,1090/1122	74450058	324,12682	2203	4300	6503	SO:0001583	missense	57835	exon25			TTATAACCGAGGG	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.3316G>A	2.37:g.74450058C>T	ENSP00000366861:p.Val1106Ile	104.0	0.0	0		82.0	47.0	0.573171	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	39	0.017857142857142856	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	14.19	2.460025	0.43736	0.00749	0.033837	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634	T;T;T;T;T;T;T	0.76968	-1.05;-0.91;-1.06;-1.06;-1.06;-0.91;-1.06	5.92	5.05	0.67936	.	0.542606	0.16548	N	0.209601	T	0.46190	0.1380	L	0.46157	1.445	0.80722	D	1	B;B;B;B	0.14805	0.011;0.004;0.003;0.001	B;B;B;B	0.14023	0.01;0.004;0.002;0.002	T	0.55211	-0.8176	10	0.15066	T	0.55	.	11.2264	0.48886	0.0:0.9158:0.0:0.0842	rs36081793	1009;988;1106;1090	Q9BY07-4;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;S4A5_HUMAN;.	I	1090;1111;1009;988;988;1106;1009;1106	ENSP00000377587:V1090I;ENSP00000251768:V1009I;ENSP00000352461:V988I;ENSP00000351513:V988I;ENSP00000350475:V1106I;ENSP00000366859:V1009I;ENSP00000366861:V1106I	ENSP00000251768:V1009I	V	-	1	0	SLC4A5	74303566	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.684000	0.25364	1.515000	0.48885	-0.150000	0.13652	GTT	C|0.977;T|0.023	0.023	strong		0.418	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651150	1651150	+	Missense_Mutation	SNP	G	G	A	rs201376522	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1651150G>A	ENST00000399676.2	+	1	118	c.80G>A	c.(79-81)gGc>gAc	p.G27D		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	27						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		tgtggctccggctgtggaggc	0.711													-|||	5	0.000998403	0.0	0.0072	5008	,	,		8675	0.0		0.0	False		,,,				2504	0.0				p.G27D		Atlas-SNP	.											KRTAP5-5,right_upper_lobe,carcinoma,-1,2	KRTAP5-5	86	2	0			c.G80A						PASS	.	G	ASP/GLY	1,4273		0,1,2136	29.0	40.0	36.0		80	3.0	0.1	11		36	4,8460		0,4,4228	no	missense	KRTAP5-5	NM_001001480.2	94	0,5,6364	AA,AG,GG		0.0473,0.0234,0.0393	benign	27/238	1651150	5,12733	2137	4232	6369	SO:0001583	missense	439915	exon1			GCTCCGGCTGTGG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.80G>A	11.37:g.1651150G>A	ENSP00000382584:p.Gly27Asp	56.0	0.0	0		55.0	38.0	0.690909	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	.	.	.	.	.	.	.	.	.	.	G	5.003	0.186328	0.09495	2.34E-4	4.73E-4	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01159	5.25	2.97	2.97	0.34412	.	.	.	.	.	T	0.02012	0.0063	M	0.71036	2.16	0.21802	N	0.999538	B	0.33694	0.421	B	0.30029	0.11	T	0.34976	-0.9807	9	0.44086	T	0.13	.	11.376	0.49728	0.0:0.0:1.0:0.0	.	27	Q701N2	KRA55_HUMAN	D	27;25	ENSP00000382584:G27D	ENSP00000382584:G27D	G	+	2	0	KRTAP5-5	1607726	0.987000	0.35691	0.068000	0.19968	0.043000	0.13939	1.957000	0.40392	1.183000	0.42943	0.442000	0.29010	GGC	.	.	weak		0.711	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
CELSR1	9620	hgsc.bcm.edu	37	22	46761565	46761565	+	Silent	SNP	G	G	C	rs34184256	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46761565G>C	ENST00000262738.3	-	31	8321	c.8322C>G	c.(8320-8322)ctC>ctG	p.L2774L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2774					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGGACACGCCGAGCTTCTGGA	0.617													g|||	53	0.0105831	0.0	0.0086	5008	,	,		11875	0.002		0.0109	False		,,,				2504	0.0348				p.L2774L		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8322G						PASS	.	C		3,4357		0,3,2177	21.0	20.0	20.0		8322	-1.4	1.0	22	dbSNP_126	20	114,8458		1,112,4173	no	coding-synonymous	CELSR1	NM_014246.1		1,115,6350	CC,CG,GG		1.3299,0.0688,0.9047		2774/3015	46761565	117,12815	2180	4286	6466	SO:0001819	synonymous_variant	9620	exon31			CACGCCGAGCTTC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8322C>G	22.37:g.46761565G>C		103.0	0.0	0		87.0	29.0	0.333333	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.992;C|0.008	0.008	strong		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
EPHB6	2051	hgsc.bcm.edu	37	7	142561786	142561786	+	Silent	SNP	T	T	C	rs56300555	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142561786T>C	ENST00000392957.2	+	7	1015	c.228T>C	c.(226-228)caT>caC	p.H76H	EPHB6_ENST00000442129.1_Silent_p.H76H|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	76	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					AGGCATGTCATGTGGCAGGGG	0.637													T|||	32	0.00638978	0.0015	0.0058	5008	,	,		16121	0.0		0.0219	False		,,,				2504	0.0041				p.H76H		Atlas-SNP	.											.	EPHB6	168	.	0			c.T228C						PASS	.	T		15,4389	21.2+/-45.6	0,15,2187	125.0	134.0	131.0		228	2.3	1.0	7	dbSNP_129	131	138,8458	66.0+/-128.3	1,136,4161	no	coding-synonymous	EPHB6	NM_004445.3		1,151,6348	CC,CT,TT		1.6054,0.3406,1.1769		76/1022	142561786	153,12847	2202	4298	6500	SO:0001819	synonymous_variant	2051	exon7			ATGTCATGTGGCA	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.228T>C	7.37:g.142561786T>C		171.0	0.0	0		143.0	73.0	0.51049	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			T|0.990;C|0.010	0.010	strong		0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38883000	38883000	+	Silent	SNP	C	C	T	rs150857304	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38883000C>T	ENST00000359357.3	+	66	9590	c.9336C>T	c.(9334-9336)agC>agT	p.S3112S	DNAH8_ENST00000449981.2_Silent_p.S3329S|DNAH8_ENST00000441566.1_Silent_p.S3076S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3112	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TCACAGTAAGCGCTCAGGCTT	0.353													C|||	4	0.000798722	0.0	0.0	5008	,	,		15337	0.001		0.002	False		,,,				2504	0.001				p.S3329S		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C9987T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	60.0	60.0	60.0		9987	3.0	1.0	6	dbSNP_134	60	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous	DNAH8	NM_001206927.1		0,33,6470	TT,TC,CC		0.3605,0.0454,0.2537		3329/4708	38883000	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon68			AGTAAGCGCTCAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.9336C>T	6.37:g.38883000C>T		89.0	0.0	0		103.0	79.0	0.76699	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.998;T|0.002	0.002	strong		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
BIVM	54841	hgsc.bcm.edu	37	13	103460019	103460019	+	Silent	SNP	G	G	A	rs111947510	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103460019G>A	ENST00000257336.1	+	3	1081	c.402G>A	c.(400-402)ctG>ctA	p.L134L	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.G106R|BIVM_ENST00000419638.1_Silent_p.L134L|BIVM_ENST00000448849.2_Intron	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	134						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CCAACAGCCTGGGCAAGCTAC	0.403													G|||	29	0.00579073	0.0219	0.0	5008	,	,		20084	0.0		0.0	False		,,,				2504	0.0				p.L134L		Atlas-SNP	.											.	.	.	.	0			c.G402A						PASS	.	G	,,	97,4309	73.6+/-111.7	4,89,2110	41.0	42.0	42.0		,402,402	2.3	1.0	13	dbSNP_132	42	0,8600		0,0,4300	no	intron,coding-synonymous,coding-synonymous	BIVM,BIVM-ERCC5	NM_001159596.1,NM_001204425.1,NM_017693.3	,,	4,89,6410	AA,AG,GG		0.0,2.2015,0.7458	,,	,134/1641,134/504	103460019	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	0	exon1			CAGCCTGGGCAAG	AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.402G>A	13.37:g.103460019G>A		89.0	0.0	0		66.0	21.0	0.318182	NM_001204425	Q2M1J2|Q9NXM4	Silent	SNP	ENST00000257336.1	37	CCDS9505.1																																																																																			G|0.991;A|0.009	0.009	strong		0.403	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2		
SERBP1	26135	hgsc.bcm.edu	37	1	67895758	67895758	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67895758T>G	ENST00000370995.2	-	1	311	c.226A>C	c.(226-228)Aaa>Caa	p.K76Q	SERBP1_ENST00000361219.6_Missense_Mutation_p.K76Q|SERBP1_ENST00000370990.5_Missense_Mutation_p.K76Q|SERBP1_ENST00000370994.4_Missense_Mutation_p.K76Q			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	76					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						TTGCGGTCTTTCTGGGACTCC	0.667																																					p.K76Q		Atlas-SNP	.											.	SERBP1	31	.	0			c.A226C						PASS	.						45.0	55.0	52.0					1																	67895758		2195	4283	6478	SO:0001583	missense	26135	exon1			GGTCTTTCTGGGA	AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.226A>C	1.37:g.67895758T>G	ENSP00000360034:p.Lys76Gln	169.0	0.0	0		149.0	50.0	0.33557	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614731	0.87359	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	4.99	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.70124	0.3188	M	0.74389	2.26	0.50632	D	0.999889	P;D;D;D	0.89917	0.818;1.0;1.0;1.0	B;D;D;D	0.85130	0.198;0.996;0.997;0.997	T	0.72633	-0.4234	9	0.52906	T	0.07	.	10.7053	0.45952	0.1426:0.0:0.0:0.8574	.	139;139;76;76	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	Q	76	.	ENSP00000354591:K76Q	K	-	1	0	SERBP1	67668346	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.400000	0.59709	2.000000	0.58554	0.379000	0.24179	AAA	.	.	none		0.667	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067	
CARHSP1	23589	hgsc.bcm.edu	37	16	8953030	8953030	+	Silent	SNP	C	C	T	rs2231706	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:8953030C>T	ENST00000396593.2	-	2	515	c.156G>A	c.(154-156)tcG>tcA	p.S52S	CARHSP1_ENST00000567554.1_Silent_p.S52S|CARHSP1_ENST00000311052.5_Silent_p.S52S|CARHSP1_ENST00000561530.1_Silent_p.S52S|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567626.1_5'Flank|CARHSP1_ENST00000562843.1_Silent_p.S52S	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	52					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						AGACTCACGCCGAGAAGGTCC	0.642													C|||	31	0.0061901	0.003	0.0014	5008	,	,		19388	0.0		0.0249	False		,,,				2504	0.001				p.S52S		Atlas-SNP	.											.	CARHSP1	12	.	0			c.G156A						PASS	.	C	,	11,4379		0,11,2184	25.0	21.0	22.0		156,156	-10.7	0.1	16	dbSNP_98	22	158,8440		0,158,4141	no	coding-synonymous,coding-synonymous	CARHSP1	NM_001042476.1,NM_014316.2	,	0,169,6325	TT,TC,CC		1.8376,0.2506,1.3012	,	52/148,52/148	8953030	169,12819	2195	4299	6494	SO:0001819	synonymous_variant	23589	exon2			TCACGCCGAGAAG	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"""calcium regulated heat stable protein 1 (24kD)"""			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.156G>A	16.37:g.8953030C>T		124.0	0.0	0		141.0	63.0	0.446809	NM_001042476	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Silent	SNP	ENST00000396593.2	37	CCDS10537.1																																																																																			C|0.989;T|0.011	0.011	strong		0.642	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316	
GATA2	2624	hgsc.bcm.edu	37	3	128204641	128204641	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128204641G>T	ENST00000341105.2	-	3	1131	c.800C>A	c.(799-801)cCc>cAc	p.P267H	GATA2_ENST00000430265.2_Missense_Mutation_p.P267H|GATA2_ENST00000487848.1_Missense_Mutation_p.P267H	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	267					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|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)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		GAAGCCTCCGGGGTGGAAGAG	0.647			Mis		AML(CML blast transformation)																																p.P267H		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C800A						PASS	.						38.0	43.0	41.0					3																	128204641		2203	4300	6503	SO:0001583	missense	2624	exon3			CCTCCGGGGTGGA	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.800C>A	3.37:g.128204641G>T	ENSP00000345681:p.Pro267His	94.0	0.0	0		102.0	31.0	0.303922	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.431859	0.83776	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97642	-4.46;-4.47;-4.46	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.98040	0.9354	M	0.69463	2.115	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.91635	0.999;0.894	D	0.98494	1.0611	10	0.48119	T	0.1	-13.2977	17.4411	0.87565	0.0:0.0:1.0:0.0	.	267;267	P23769-2;P23769	.;GATA2_HUMAN	H	267	ENSP00000345681:P267H;ENSP00000400259:P267H;ENSP00000417074:P267H	ENSP00000345681:P267H	P	-	2	0	GATA2	129687331	1.000000	0.71417	0.924000	0.36721	0.808000	0.45660	7.843000	0.86859	2.099000	0.63709	0.491000	0.48974	CCC	.	.	none		0.647	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
SLC44A3	126969	hgsc.bcm.edu	37	1	95330440	95330440	+	Silent	SNP	C	C	T	rs142406496	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:95330440C>T	ENST00000271227.6	+	11	1482	c.1380C>T	c.(1378-1380)aaC>aaT	p.N460N	SLC44A3_ENST00000467909.1_Silent_p.N412N|SLC44A3_ENST00000446120.2_Silent_p.N424N|SLC44A3_ENST00000529450.1_Silent_p.N428N|SLC44A3_ENST00000532427.1_Silent_p.N380N|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000527077.1_Silent_p.N392N	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	460					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	ACATGCAAAACGCACTGAAAG	0.438													C|||	10	0.00199681	0.0	0.0014	5008	,	,		19243	0.001		0.008	False		,,,				2504	0.0				p.N460N		Atlas-SNP	.											.	SLC44A3	109	.	0			c.C1380T						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	201.0	187.0	192.0		1380,1236	4.9	0.0	1	dbSNP_134	192	47,8553	31.7+/-84.0	0,47,4253	no	coding-synonymous,coding-synonymous	SLC44A3	NM_001114106.1,NM_152369.3	,	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	,	460/654,412/606	95330440	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	126969	exon11			GCAAAACGCACTG	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1380C>T	1.37:g.95330440C>T		83.0	0.0	0		99.0	51.0	0.515152	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			C|0.996;T|0.004	0.004	strong		0.438	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
PROC	5624	hgsc.bcm.edu	37	2	128178900	128178900	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:128178900C>T	ENST00000234071.3	+	3	199	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W	PROC_ENST00000453608.2_Missense_Mutation_p.R59W|MIR4783_ENST00000580343.1_RNA|PROC_ENST00000422777.3_Missense_Mutation_p.R38W|PROC_ENST00000409048.1_Missense_Mutation_p.R38W	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	38			R -> W (in patients with PROC deficiency). {ECO:0000269|PubMed:8324221}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCAGGTGCTGCGGATCCGCAA	0.632																																					p.R38W		Atlas-SNP	.											PROC,colon,carcinoma,-1,1	PROC	31	1	0			c.C112T	GRCh37	CM930605	PROC	M		PASS	.						81.0	73.0	76.0					2																	128178900		2203	4300	6503	SO:0001583	missense	5624	exon3			GTGCTGCGGATCC	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"""Endogenous ligands"""	9451	protein-coding gene	gene with protein product	"""prepro-protein C"""	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.112C>T	2.37:g.128178900C>T	ENSP00000234071:p.Arg38Trp	202.0	0.0	0		127.0	47.0	0.370079	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Missense_Mutation	SNP	ENST00000234071.3	37	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511314	0.64522	.	.	ENSG00000115718	ENST00000234071;ENST00000429925;ENST00000442644;ENST00000453608;ENST00000427769;ENST00000409048;ENST00000422777	D;D;D;D;D;D;D	0.99709	-3.09;-5.96;-6.48;-3.17;-5.65;-3.14;-3.09	5.2	3.17	0.36434	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.000000	0.38436	N	0.001686	D	0.99429	0.9798	L	0.54323	1.7	0.40797	D	0.983301	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.988;0.995;0.988;0.988	D	0.98660	1.0683	10	0.87932	D	0	.	11.6367	0.51209	0.6041:0.3959:0.0:0.0	.	59;59;38;38	B4DPQ7;B4DPQ3;E7END6;P04070	.;.;.;PROC_HUMAN	W	38;38;38;59;38;38;38	ENSP00000234071:R38W;ENSP00000412697:R38W;ENSP00000411241:R38W;ENSP00000404030:R59W;ENSP00000406295:R38W;ENSP00000386679:R38W;ENSP00000409543:R38W	ENSP00000234071:R38W	R	+	1	2	PROC	127895370	0.992000	0.36948	0.598000	0.28837	0.506000	0.33950	2.484000	0.45242	1.156000	0.42514	0.561000	0.74099	CGG	.	.	none		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
ELP3	55140	hgsc.bcm.edu	37	8	27957438	27957438	+	Silent	SNP	C	C	T	rs200001470	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27957438C>T	ENST00000256398.8	+	3	590	c.213C>T	c.(211-213)gtC>gtT	p.V71V	ELP3_ENST00000380353.4_Intron|ELP3_ENST00000524103.1_5'UTR|ELP3_ENST00000521015.1_Silent_p.V57V|ELP3_ENST00000542181.1_Intron|ELP3_ENST00000523760.1_3'UTR|ELP3_ENST00000537665.1_5'UTR	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	71					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		ATCGCAAGGTCTTGATGCCCA	0.522													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20896	0.0		0.0	False		,,,				2504	0.0				p.V71V		Atlas-SNP	.											.	ELP3	36	.	0			c.C213T						PASS	.	C		0,4406		0,0,2203	144.0	119.0	127.0		213	3.5	1.0	8		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ELP3	NM_018091.5		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		71/548	27957438	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55140	exon3			CAAGGTCTTGATG		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Elongator acetyltransferase complex subunits"""	20696	protein-coding gene	gene with protein product		612722	"""elongation protein 3 homolog (S. cerevisiae)"""			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.213C>T	8.37:g.27957438C>T		60.0	0.0	0		65.0	27.0	0.415385	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Silent	SNP	ENST00000256398.8	37	CCDS6065.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091	
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44495953A>G	ENST00000338758.7	+	3	286	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V|PARVB_ENST00000477795.1_3'UTR	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	75					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGAGCGCACGATGATTGACCC	0.572													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18925	0.0		0.002	False		,,,				2504	0.0				p.M108V		Atlas-SNP	.											.	PARVB	44	.	0			c.A322G						PASS	.	A	VAL/MET,VAL/MET	4,4402	8.1+/-20.4	0,4,2199	123.0	100.0	108.0		322,223	3.5	0.9	22	dbSNP_129	108	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	21,21	0,39,6464	GG,GA,AA		0.407,0.0908,0.2999	benign,benign	108/398,75/365	44495953	39,12967	2203	4300	6503	SO:0001583	missense	29780	exon4			CGCACGATGATTG	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.223A>G	22.37:g.44495953A>G	ENSP00000342492:p.Met75Val	79.0	0.0	0		66.0	35.0	0.530303	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	12.33	1.905546	0.33628	9.08E-4	0.00407	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	4.5	3.45	0.39498	Calponin homology domain (1);	0.131379	0.64402	N	0.000001	T	0.31513	0.0799	L	0.52905	1.665	0.47511	D	0.999442	B;B;B;B	0.16166	0.005;0.001;0.003;0.016	B;B;B;B	0.23018	0.006;0.005;0.008;0.043	T	0.07908	-1.0748	10	0.40728	T	0.16	-2.8779	7.5657	0.27876	0.8909:0.0:0.1091:0.0	rs56194750	75;38;75;108	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	V	108;75;75;73;38	ENSP00000384515:M108V;ENSP00000342492:M75V;ENSP00000385331:M75V;ENSP00000393758:M73V;ENSP00000384353:M38V	ENSP00000342492:M75V	M	+	1	0	PARVB	42827286	1.000000	0.71417	0.919000	0.36401	0.989000	0.77384	4.938000	0.63519	0.585000	0.29608	0.460000	0.39030	ATG	A|0.997;G|0.003	0.003	strong		0.572	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42662976A>C	ENST00000232978.8	+	6	530	c.342A>C	c.(340-342)cgA>cgC	p.R114R	RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	114	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TGGCAAATCGAGGGAAACATA	0.358													A|||	35	0.00698882	0.0083	0.0072	5008	,	,		15576	0.0		0.0179	False		,,,				2504	0.001				p.R114R		Atlas-SNP	.											.	NKTR	116	.	0			c.A342C						PASS	.	A		32,4374	39.2+/-71.8	0,32,2171	76.0	73.0	74.0		342	-1.8	1.0	3	dbSNP_126	74	128,8470	65.6+/-127.9	1,126,4172	no	coding-synonymous	NKTR	NM_005385.3		1,158,6343	CC,CA,AA		1.4887,0.7263,1.2304		114/1463	42662976	160,12844	2203	4299	6502	SO:0001819	synonymous_variant	4820	exon6			AAATCGAGGGAAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.342A>C	3.37:g.42662976A>C		67.0	0.0	0		78.0	29.0	0.371795	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			A|0.988;C|0.012	0.012	strong		0.358	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
COL24A1	255631	hgsc.bcm.edu	37	1	86488270	86488270	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86488270T>G	ENST00000370571.2	-	17	2519	c.2153A>C	c.(2152-2154)gAa>gCa	p.E718A	COL24A1_ENST00000436319.1_Missense_Mutation_p.E718A	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	718	Collagen-like 3.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TGTGCCTTGTTCACCCTGGAA	0.333																																					p.E718A		Atlas-SNP	.											.	COL24A1	202	.	0			c.A2153C						PASS	.						62.0	62.0	62.0					1																	86488270		1866	4098	5964	SO:0001583	missense	255631	exon17			CCTTGTTCACCCT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.2153A>C	1.37:g.86488270T>G	ENSP00000359603:p.Glu718Ala	148.0	0.0	0		166.0	16.0	0.0963855	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.376743	0.42105	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.93488	-3.23;-3.23	5.62	5.62	0.85841	.	0.000000	0.37348	N	0.002132	D	0.91546	0.7330	L	0.33189	0.99	0.49687	D	0.999816	D	0.63880	0.993	D	0.65140	0.932	D	0.90183	0.4244	10	0.22109	T	0.4	.	14.0686	0.64847	0.0:0.0:0.0:1.0	.	718	Q17RW2	COOA1_HUMAN	A	718	ENSP00000359603:E718A;ENSP00000392531:E718A	ENSP00000359603:E718A	E	-	2	0	COL24A1	86260858	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.078000	0.57606	2.129000	0.65627	0.533000	0.62120	GAA	.	.	none		0.333	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
B3GNT5	84002	hgsc.bcm.edu	37	3	182987591	182987591	+	Missense_Mutation	SNP	G	G	A	rs115825683	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182987591G>A	ENST00000326505.3	+	2	535	c.5G>A	c.(4-6)aGa>aAa	p.R2K	MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.R2K|B3GNT5_ENST00000460419.1_Missense_Mutation_p.R2K|MCF2L2_ENST00000473233.1_Intron	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	2					cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycolipid biosynthetic process (GO:0009247)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity (GO:0008457)|galactosyltransferase activity (GO:0008378)|lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity (GO:0047256)|lipopolysaccharide N-acetylglucosaminyltransferase activity (GO:0008917)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			GTGGATATGAGAATGTTGGTT	0.388													g|||	17	0.00339457	0.0	0.0029	5008	,	,		19069	0.0		0.0099	False		,,,				2504	0.0051				p.R2K		Atlas-SNP	.											.	B3GNT5	26	.	0			c.G5A						PASS	.		,LYS/ARG	7,4399	12.9+/-30.5	0,7,2196	113.0	113.0	113.0		,5	5.6	1.0	3	dbSNP_132	113	118,8482	61.7+/-123.6	2,114,4184	yes	intron,missense	MCF2L2,B3GNT5	NM_015078.2,NM_032047.4	,26	2,121,6380	AA,AG,GG		1.3721,0.1589,0.9611	,benign	,2/379	182987591	125,12881	2203	4300	6503	SO:0001583	missense	84002	exon2			ATATGAGAATGTT	AB045278	CCDS3244.1	3q28	2013-02-21			ENSG00000176597	ENSG00000176597	2.4.1.206	"""Beta 3-glycosyltransferases"""	15684	protein-coding gene	gene with protein product	"""lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase"""	615333				11283017	Standard	XM_005247824		Approved	B3GN-T5, beta3Gn-T5	uc003flk.3	Q9BYG0	OTTHUMG00000158436	ENST00000326505.3:c.5G>A	3.37:g.182987591G>A	ENSP00000316173:p.Arg2Lys	69.0	0.0	0		63.0	26.0	0.412698	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	37	CCDS3244.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	15.44	2.833998	0.50951	0.001589	0.013721	ENSG00000176597	ENST00000326505;ENST00000464191;ENST00000460419;ENST00000464923;ENST00000465010;ENST00000481531	T;T;T	0.37915	1.17;1.17;1.17	5.62	5.62	0.85841	.	0.575937	0.18329	N	0.144543	T	0.43411	0.1246	L	0.57536	1.79	0.33902	D	0.638687	D	0.60575	0.988	P	0.52343	0.696	T	0.60209	-0.7308	10	0.87932	D	0	.	20.0252	0.97521	0.0:0.0:1.0:0.0	.	2	Q9BYG0	B3GN5_HUMAN	K	2	ENSP00000316173:R2K;ENSP00000420778:R2K;ENSP00000417868:R2K	ENSP00000316173:R2K	R	+	2	0	B3GNT5	184470285	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	2.861000	0.48380	2.801000	0.96364	0.651000	0.88453	AGA	G|0.994;A|0.006	0.006	strong		0.388	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047	
GPD2	2820	hgsc.bcm.edu	37	2	157367399	157367399	+	Silent	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:157367399G>T	ENST00000310454.6	+	4	738	c.366G>T	c.(364-366)ctG>ctT	p.L122L	GPD2_ENST00000409674.1_Silent_p.L122L|GPD2_ENST00000438166.2_Silent_p.L122L|GPD2_ENST00000409125.4_Intron|GPD2_ENST00000540309.1_Silent_p.L122L	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	122					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGAGATATCTGCAGAAGGCCA	0.403																																					p.L122L		Atlas-SNP	.											.	GPD2	59	.	0			c.G366T						PASS	.						179.0	177.0	178.0					2																	157367399		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon4			ATATCTGCAGAAG		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"""EF-hand domain containing"""	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.366G>T	2.37:g.157367399G>T		199.0	1.0	0.00502513		144.0	107.0	0.743056	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	37	CCDS2202.1																																																																																			.	.	none		0.403	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
CASZ1	54897	hgsc.bcm.edu	37	1	10705018	10705018	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10705018T>C	ENST00000377022.3	-	18	4141	c.3824A>G	c.(3823-3825)aAt>aGt	p.N1275S	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1275					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TTTGAAGCCATTGGCTGCCCG	0.607																																					p.N1275S		Atlas-SNP	.											.	CASZ1	150	.	0			c.A3824G						PASS	.						63.0	74.0	70.0					1																	10705018		2042	4191	6233	SO:0001583	missense	54897	exon18			AAGCCATTGGCTG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.3824A>G	1.37:g.10705018T>C	ENSP00000366221:p.Asn1275Ser	103.0	0.0	0		81.0	40.0	0.493827	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536822	0.85812	.	.	ENSG00000130940	ENST00000377022	.	.	.	5.15	5.15	0.70609	.	0.000000	0.48286	U	0.000188	T	0.62295	0.2416	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.64411	-0.6414	9	0.41790	T	0.15	-21.2576	14.9882	0.71365	0.0:0.0:0.0:1.0	.	1275	Q86V15	CASZ1_HUMAN	S	1275	.	ENSP00000366221:N1275S	N	-	2	0	CASZ1	10627605	1.000000	0.71417	0.934000	0.37439	0.979000	0.70002	8.040000	0.89188	1.943000	0.56356	0.459000	0.35465	AAT	.	.	none		0.607	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
VCX3B	425054	hgsc.bcm.edu	37	X	8434346	8434346	+	Silent	SNP	G	G	A	rs808146		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:8434346G>A	ENST00000381032.1	+	3	970	c.663G>A	c.(661-663)gaG>gaA	p.E221E	VCX3B_ENST00000381029.4_Silent_p.E189E|VCX3B_ENST00000440654.2_Silent_p.E171E|VCX3B_ENST00000453306.1_Intron|VCX3B_ENST00000444481.1_Silent_p.E191E	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	221	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						GCCAGGTGGAGGAACCACTGA	0.557																																					p.E221E		Atlas-SNP	.											.	VCX3B	34	.	0			c.G663A						PASS	.	G		1,3807		0,0,1,1626,555	90.0	176.0	147.0		663	-1.1	0.0	X	dbSNP_86	147	8,6662		1,5,1,2418,1821	no	coding-synonymous	VCX3B	NM_001001888.3		1,5,2,4044,2376	AA,AG,A,GG,G		0.1199,0.0263,0.0859		221/247	8434346	9,10469	2182	4246	6428	SO:0001819	synonymous_variant	425054	exon3			GGTGGAGGAACCA		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.663G>A	X.37:g.8434346G>A		326.0	0.0	0		450.0	135.0	0.3	NM_001001888	C9JS46|Q4KN12	Silent	SNP	ENST00000381032.1	37	CCDS48077.2																																																																																			.	.	weak		0.557	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1		
YBX1	4904	hgsc.bcm.edu	37	1	43149084	43149084	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43149084T>C	ENST00000321358.7	+	2	316	c.177T>C	c.(175-177)gtT>gtC	p.V59V	YBX1_ENST00000467957.1_3'UTR|RP5-994D16.3_ENST00000414339.1_lincRNA	NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	59	Interaction with ss-DNA.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CAACGAAGGTTTTGGGAACAG	0.502																																					p.V59V		Atlas-SNP	.											.	YBX1	49	.	0			c.T177C						PASS	.						92.0	95.0	94.0					1																	43149084		2203	4300	6503	SO:0001819	synonymous_variant	4904	exon2			GAAGGTTTTGGGA	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"""nuclease sensitive element binding protein 1"""	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.177T>C	1.37:g.43149084T>C		104.0	0.0	0		104.0	28.0	0.269231	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Silent	SNP	ENST00000321358.7	37	CCDS470.1																																																																																			.	.	none		0.502	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559	
AKAP3	10566	hgsc.bcm.edu	37	12	4735922	4735922	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4735922C>G	ENST00000545990.2	-	5	2670	c.2146G>C	c.(2146-2148)Gag>Cag	p.E716Q	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.E716Q	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	716					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GGTAAGCACTCATATAAACTA	0.507																																					p.E716Q		Atlas-SNP	.											.	AKAP3	212	.	0			c.G2146C						PASS	.						67.0	60.0	62.0					12																	4735922		2203	4300	6503	SO:0001583	missense	10566	exon4			AGCACTCATATAA	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2146G>C	12.37:g.4735922C>G	ENSP00000440994:p.Glu716Gln	98.0	0.0	0		112.0	30.0	0.267857	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	9.085	1.000286	0.19121	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.08282	3.11;3.11	4.91	4.91	0.64330	A-kinase anchor 110kDa, C-terminal (1);	0.111221	0.40144	N	0.001163	T	0.19886	0.0478	M	0.63428	1.95	0.27479	N	0.952633	D	0.56746	0.977	P	0.59357	0.856	T	0.02196	-1.1197	10	0.45353	T	0.12	-22.7839	10.643	0.45604	0.1911:0.8089:0.0:0.0	.	716	O75969	AKAP3_HUMAN	Q	716	ENSP00000228850:E716Q;ENSP00000440994:E716Q	ENSP00000228850:E716Q	E	-	1	0	AKAP3	4606183	0.884000	0.30299	0.652000	0.29579	0.024000	0.10985	2.160000	0.42348	2.544000	0.85801	0.655000	0.94253	GAG	.	.	none		0.507	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
DEFB110	245913	hgsc.bcm.edu	37	6	49986738	49986738	+	Silent	SNP	C	C	T	rs115648436	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49986738C>T	ENST00000371148.2	-	2	201	c.156G>A	c.(154-156)agG>agA	p.R52R	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	52					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					AGTAAGCAATCCTAATTTCAT	0.403													C|||	30	0.00599042	0.0008	0.0115	5008	,	,		21326	0.0		0.0209	False		,,,				2504	0.0				p.R52R		Atlas-SNP	.											.	DEFB110	5	.	0			c.G156A						PASS	.	C	,	14,4392	19.1+/-41.9	0,14,2189	164.0	139.0	147.0		156,	-4.2	0.9	6	dbSNP_132	147	129,8471	66.3+/-128.7	0,129,4171	no	coding-synonymous,intron	DEFB110	NM_001037497.1,NM_001037728.2	,	0,143,6360	TT,TC,CC		1.5,0.3177,1.0995	,	52/68,	49986738	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	245913	exon2			AGCAATCCTAATT	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.156G>A	6.37:g.49986738C>T		159.0	0.0	0		132.0	65.0	0.492424	NM_001037497	Q30KR0	Silent	SNP	ENST00000371148.2	37	CCDS34475.1																																																																																			C|0.991;T|0.009	0.009	strong		0.403	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11009679G>A	ENST00000377008.4	-	10	1236		c.e10+1		C1orf127_ENST00000377004.4_Splice_Site			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCATAGACGTGCTTTGGCCAG	0.612													G|||	346	0.0690895	0.2035	0.0144	5008	,	,		17717	0.004		0.0427	False		,,,				2504	0.0204				.		Atlas-SNP	.											.	C1orf127	134	.	0			c.1290+2C>T						PASS	.	G		719,3679		64,591,1544	34.0	29.0	31.0			-0.6	0.0	1	dbSNP_87	31	331,8269		4,323,3973	yes	splice-5	C1orf127	NM_001170754.1		68,914,5517	AA,AG,GG		3.8488,16.3483,8.0782			11009679	1050,11948	2199	4300	6499	SO:0001630	splice_region_variant	148345	exon12			AGACGTGCTTTGG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.789+1C>T	1.37:g.11009679G>A		56.0	0.0	0		51.0	29.0	0.568627	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Splice_Site	SNP	ENST00000377008.4	37		166	0.076007326007326	122	0.24796747967479674	4	0.011049723756906077	1	0.0017482517482517483	39	0.051451187335092345	G	2.596	-0.293985	0.05568	0.163483	0.038488	ENSG00000175262	ENST00000418570;ENST00000377004;ENST00000377008	.	.	.	3.68	-0.578	0.11724	.	.	.	.	.	.	.	.	.	.	.	0.51012	P	9.899999999996023E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.2328	0.01946	0.2149:0.1807:0.4347:0.1697	rs1281013;rs1281013	.	.	.	.	-1	.	.	.	-	.	.	C1orf127	10932266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.106000	0.15354	-0.247000	0.09597	-0.354000	0.07668	.	G|0.907;A|0.093	0.093	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	Intron
LIG4	3981	hgsc.bcm.edu	37	13	108861048	108861048	+	Missense_Mutation	SNP	C	C	T	rs2232642	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:108861048C>T	ENST00000356922.4	-	2	2841	c.2569G>A	c.(2569-2571)Gct>Act	p.A857T	LIG4_ENST00000442234.1_Missense_Mutation_p.A857T|LIG4_ENST00000405925.1_Missense_Mutation_p.A857T	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	857	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.		A -> T (in dbSNP:rs2232642). {ECO:0000269|Ref.2}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ACTCCCTCAGCTAAACAAGAA	0.363								Non-homologous end-joining					C|||	177	0.0353435	0.1263	0.0144	5008	,	,		17213	0.0		0.0	False		,,,				2504	0.0				p.A857T		Atlas-SNP	.											.	LIG4	91	.	0			c.G2569A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	442,3964	211.8+/-231.9	27,388,1788	105.0	104.0	105.0		2569,2569,2569	2.9	1.0	13	dbSNP_98	105	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	58,58,58	27,392,6084	TT,TC,CC		0.0465,10.0318,3.4292	benign,benign,benign	857/912,857/912,857/912	108861048	446,12560	2203	4300	6503	SO:0001583	missense	3981	exon3			CCTCAGCTAAACA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.2569G>A	13.37:g.108861048C>T	ENSP00000349393:p.Ala857Thr	107.0	0.0	0		79.0	21.0	0.265823	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	C	14.05	2.419038	0.42918	0.100318	4.65E-4	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.77489	-1.1;-1.1;-1.1	5.75	2.86	0.33363	BRCT (4);	0.233058	0.43110	N	0.000618	T	0.00845	0.0028	L	0.44542	1.39	0.48040	P	4.2600000000003746E-4	B	0.10296	0.003	B	0.06405	0.002	T	0.12400	-1.0549	9	0.18276	T	0.48	.	6.1326	0.20213	0.1432:0.6532:0.1303:0.0734	rs2232642;rs52801587;rs2232642	857	P49917	DNLI4_HUMAN	T	857	ENSP00000385955:A857T;ENSP00000402030:A857T;ENSP00000349393:A857T	ENSP00000349393:A857T	A	-	1	0	LIG4	107659049	0.983000	0.35010	0.997000	0.53966	0.961000	0.63080	1.621000	0.36986	0.749000	0.32854	0.567000	0.79289	GCT	C|0.958;T|0.042	0.042	strong		0.363	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
ATF4	468	hgsc.bcm.edu	37	22	39917561	39917561	+	Silent	SNP	C	C	T	rs375843215		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39917561C>T	ENST00000337304.2	+	1	993	c.111C>T	c.(109-111)taC>taT	p.Y37Y	ATF4_ENST00000396680.1_Silent_p.Y37Y|ATF4_ENST00000404241.2_Silent_p.Y37Y	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	37					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	TAGATGATTACCTGGAGGTGG	0.577																																					p.Y37Y		Atlas-SNP	.											.	ATF4	27	.	0			c.C111T						PASS	.	C	,	0,4406		0,0,2203	63.0	62.0	63.0		111,111	3.3	1.0	22		63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATF4	NM_001675.2,NM_182810.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	37/352,37/352	39917561	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	468	exon1			TGATTACCTGGAG	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.111C>T	22.37:g.39917561C>T		112.0	0.0	0		100.0	45.0	0.45	NM_001675	Q9UH31	Silent	SNP	ENST00000337304.2	37	CCDS13996.1																																																																																			.	.	weak		0.577	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11008102G>A	ENST00000377008.4	-	11	2035	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A697V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	530			A -> V (in dbSNP:rs1281018).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGCCAGGGGCGCTGCCAGCCT	0.622													G|||	442	0.0882588	0.2542	0.0245	5008	,	,		18073	0.0069		0.0447	False		,,,				2504	0.0378				p.A697V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C2090T						PASS	.	G	VAL/ALA	809,3597	299.6+/-285.9	81,647,1475	36.0	38.0	37.0		2090	-2.0	0.0	1	dbSNP_87	37	346,8254	112.3+/-172.5	4,338,3958	yes	missense	C1orf127	NM_001170754.1	64	85,985,5433	AA,AG,GG		4.0233,18.3613,8.8805	possibly-damaging	697/824	11008102	1155,11851	2203	4300	6503	SO:0001583	missense	148345	exon12			AGGGGCGCTGCCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1589C>T	1.37:g.11008102G>A	ENSP00000366207:p.Ala530Val	64.0	0.0	0		71.0	37.0	0.521127	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		165|165	0.07554945054945054|0.07554945054945054	115|115	0.23373983739837398|0.23373983739837398	8|8	0.022099447513812154|0.022099447513812154	2|2	0.0034965034965034965|0.0034965034965034965	40|40	0.052770448548812667|0.052770448548812667	G|G	7.224|7.224	0.597877|0.597877	0.13939|0.13939	0.183613|0.183613	0.040233|0.040233	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.33865|.	1.39;1.39|.	3.9|3.9	-2.05|-2.05	0.07321|0.07321	.|.	0.523531|.	0.14669|.	N|.	0.305451|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	P;P;P|.	0.42961|.	0.795;0.795;0.795|.	B;B;B|.	0.31390|.	0.129;0.129;0.081|.	T|T	0.35051|0.35051	-0.9804|-0.9804	9|4	0.18276|.	T|.	0.48|.	-0.422|-0.422	0.9467|0.9467	0.01367|0.01367	0.2137:0.3268:0.2711:0.1885|0.2137:0.3268:0.2711:0.1885	rs1281018;rs1281018|rs1281018;rs1281018	548;522;530|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|C	697;530|532;649	ENSP00000366203:A697V;ENSP00000366207:A530V|.	ENSP00000366203:A697V|.	A|R	-|-	2|1	0|0	C1orf127|C1orf127	10930689|10930689	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	-2.362000|-2.362000	0.01082|0.01082	-0.266000|-0.266000	0.09339|0.09339	-0.474000|-0.474000	0.04947|0.04947	GCG|CGC	G|0.914;A|0.086	0.086	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465038	39465038	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39465038A>G	ENST00000391352.1	-	1	467	c.468T>C	c.(466-468)ccT>ccC	p.P156P		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	156	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CACAAATAGCAGGCTCACAGC	0.577																																					p.P156P		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.T468C						PASS	.																																			SO:0001819	synonymous_variant	100505753	exon1			AATAGCAGGCTCA	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.468T>C	17.37:g.39465038A>G		125.0	0.0	0		118.0	35.0	0.29661	NM_001146182		Silent	SNP	ENST00000391352.1	37	CCDS56032.1																																																																																			.	.	none		0.577	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
ALMS1	7840	hgsc.bcm.edu	37	2	73676965	73676965	+	Missense_Mutation	SNP	G	G	A	rs201074268	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73676965G>A	ENST00000264448.6	+	8	3419	c.3308G>A	c.(3307-3309)gGt>gAt	p.G1103D	ALMS1_ENST00000409009.1_Missense_Mutation_p.G1061D|ALMS1_ENST00000377715.1_Missense_Mutation_p.G1103D	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1103	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GAGAAGCCTGGTATTTTCTAC	0.488													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19306	0.0		0.003	False		,,,				2504	0.0				p.G1103D		Atlas-SNP	.											.	ALMS1	384	.	0			c.G3308A						PASS	.	G	ASP/GLY	0,3726		0,0,1863	101.0	103.0	102.0		3308	-8.9	0.0	2		102	21,8177		0,21,4078	yes	missense	ALMS1	NM_015120.4	94	0,21,5941	AA,AG,GG		0.2562,0.0,0.1761	benign	1103/4168	73676965	21,11903	1863	4099	5962	SO:0001583	missense	7840	exon8			AGCCTGGTATTTT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.3308G>A	2.37:g.73676965G>A	ENSP00000264448:p.Gly1103Asp	64.0	0.0	0		61.0	42.0	0.688525	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	2.987	-0.208957	0.06140	0.0	0.002562	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14893	3.35;3.35;2.47	4.46	-8.91	0.00778	.	3.168410	0.00654	N	0.000568	T	0.06508	0.0167	L	0.34521	1.04	0.09310	N	1	B;B;P	0.40602	0.015;0.034;0.723	B;B;B	0.41510	0.015;0.015;0.359	T	0.41233	-0.9520	10	0.06099	T	0.92	.	2.1614	0.03826	0.3512:0.0833:0.1306:0.4348	.	1103;1061;1103	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	D	1061;1103;1103	ENSP00000386627:G1061D;ENSP00000264448:G1103D;ENSP00000366944:G1103D	ENSP00000264448:G1103D	G	+	2	0	ALMS1	73530473	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.200000	0.00142	-3.469000	0.00157	-1.083000	0.02208	GGT	G|0.998;A|0.002	0.002	strong		0.488	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909507	2909507	+	Missense_Mutation	SNP	G	G	A	rs146094810	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2909507G>A	ENST00000533594.1	-	4	1161	c.665C>T	c.(664-666)cCc>cTc	p.P222L	CDKN1C_ENST00000440480.2_5'Flank|SLC22A18AS_ENST00000526203.1_Missense_Mutation_p.P119L|CDKN1C_ENST00000313407.6_5'Flank|SLC22A18AS_ENST00000455942.2_Missense_Mutation_p.P119L|CDKN1C_ENST00000414822.3_5'Flank|CDKN1C_ENST00000430149.2_5'Flank|CDKN1C_ENST00000380725.1_5'Flank	NM_007105.2	NP_009036.2	Q8N1D0	BWR1B_HUMAN	solute carrier family 22 (organic cation transporter), member 18 antisense	222										NS(1)|endometrium(2)	3						CGCGGGGTTGGGGGGGCGGGG	0.622											OREG0020687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0023	0.0072	5008	,	,		10396	0.0		0.001	False		,,,				2504	0.0				p.P222L		Atlas-SNP	.											.	SLC22A18AS	7	.	0			c.C665T						PASS	.						13.0	14.0	14.0					11																	2909507		692	1591	2283	SO:0001583	missense	5003	exon4			GGGTTGGGGGGGC	AF035407	CCDS7739.1	11p15.5	2011-02-10	2005-08-23	2005-08-23	ENSG00000254827	ENSG00000254827			10965	protein-coding gene	gene with protein product		603240	"""solute carrier family 22 (organic cation transporter), member 1-like antisense"""	BWSCR1B, ORCTL2S, SLC22A1LS		9570947, 9520460, 15175115	Standard	NM_007105		Approved	BWR1B, p27-BWR1B	uc001lwv.4	Q8N1D0	OTTHUMG00000010038	ENST00000533594.1:c.665C>T	11.37:g.2909507G>A	ENSP00000433282:p.Pro222Leu	49.0	0.0	0	607	60.0	33.0	0.55	NM_007105	E9PLK8|O43563	Missense_Mutation	SNP	ENST00000533594.1	37	CCDS7739.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	7.937	0.741844	0.15642	.	.	ENSG00000254827	ENST00000533594;ENST00000526203;ENST00000455942	T;T;T	0.57273	1.0;0.41;0.41	0.62	0.62	0.17637	.	.	.	.	.	T	0.40322	0.1112	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.76575	0.988	T	0.35076	-0.9803	8	0.87932	D	0	.	.	.	.	.	222	E9PLK8	.	L	222;119;119	ENSP00000433282:P222L;ENSP00000435592:P119L;ENSP00000434027:P119L	ENSP00000434027:P119L	P	-	2	0	SLC22A18AS	2866083	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.367000	0.07553	0.576000	0.29452	0.205000	0.17691	CCC	G|0.998;A|0.002	0.002	strong		0.622	SLC22A18AS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027771.3	NM_007105	
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	A	rs141028225		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495169G>A	ENST00000237305.7	-	3	290	c.202C>T	c.(202-204)Ctt>Ttt	p.L68F	SGK1_ENST00000528577.1_Missense_Mutation_p.L96F|SGK1_ENST00000413996.3_Missense_Mutation_p.L82F|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.L58F|SGK1_ENST00000475719.2_Missense_Mutation_p.L68F|SGK1_ENST00000367858.5_Missense_Mutation_p.L163F	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	68					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GCATTCATAAGCTCAGGCTCC	0.478																																					p.L163F		Atlas-SNP	.											.	SGK1	387	.	0			c.C487T						PASS	.						151.0	144.0	146.0					6																	134495169		2203	4300	6503	SO:0001583	missense	6446	exon5			TCATAAGCTCAGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.202C>T	6.37:g.134495169G>A	ENSP00000237305:p.Leu68Phe	80.0	0.0	0		72.0	21.0	0.291667	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292643	0.40594	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72942	-0.69;-0.7;-0.67;-0.68;-0.67;-0.67	5.99	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.57489	0.2057	L	0.54323	1.7	0.80722	D	1	P;P;B;P;P;P	0.44380	0.825;0.834;0.0;0.571;0.573;0.595	B;B;B;B;B;B	0.44163	0.443;0.234;0.001;0.252;0.325;0.142	T	0.64019	-0.6505	10	0.56958	D	0.05	.	11.0283	0.47757	0.1506:0.0:0.8494:0.0	.	96;82;68;58;163;68	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	F	163;82;68;58;96;68;132	ENSP00000356832:L163F;ENSP00000396242:L82F;ENSP00000237305:L68F;ENSP00000356831:L58F;ENSP00000434450:L96F;ENSP00000434302:L68F	ENSP00000237305:L68F	L	-	1	0	SGK1	134536862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.307000	0.51888	1.377000	0.46286	0.655000	0.94253	CTT	G|1.000;C|0.000	.	alt		0.478	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
NCAPD2	9918	hgsc.bcm.edu	37	12	6630996	6630996	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6630996C>T	ENST00000315579.5	+	15	2546	c.1747C>T	c.(1747-1749)Cgg>Tgg	p.R583W	NCAPD2_ENST00000545962.1_Missense_Mutation_p.R538W	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	583	Interactions with SMC2 and SMC4.				mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AAAGAATCCCCGGGAGTCTAC	0.468																																					p.R583W		Atlas-SNP	.											NCAPD2,NS,carcinoma,0,1	NCAPD2	99	1	0			c.C1747T						PASS	.						69.0	72.0	71.0					12																	6630996		2203	4300	6503	SO:0001583	missense	9918	exon15			AATCCCCGGGAGT	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.1747C>T	12.37:g.6630996C>T	ENSP00000325017:p.Arg583Trp	70.0	0.0	0		66.0	21.0	0.318182	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.729860	0.30684	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.31247	2.5;1.5;2.23	5.3	5.3	0.74995	Armadillo-type fold (1);	1.094420	0.06897	N	0.805353	T	0.21674	0.0522	N	0.08118	0	0.09310	N	1	D;P;P	0.56968	0.978;0.733;0.912	B;B;B	0.40101	0.319;0.17;0.17	T	0.42396	-0.9454	10	0.66056	D	0.02	-0.0214	15.8787	0.79185	0.0:1.0:0.0:0.0	.	538;544;583	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	W	583;455;538;455	ENSP00000325017:R583W;ENSP00000371895:R455W;ENSP00000444417:R538W	ENSP00000325017:R583W	R	+	1	2	NCAPD2	6501257	0.858000	0.29795	0.012000	0.15200	0.004000	0.04260	2.584000	0.46102	2.480000	0.83734	0.467000	0.42956	CGG	.	.	none		0.468	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48312084G>C	ENST00000435803.1	+	17	2845	c.2821G>C	c.(2821-2823)Gtt>Ctt	p.V941L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	941					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAAACAAGAAGTTGATAAAAT	0.368													G|||	126	0.0251597	0.003	0.0202	5008	,	,		17420	0.0		0.0557	False		,,,				2504	0.0532				p.V941L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2821C						PASS	.	G	LEU/VAL	45,3611		0,45,1783	58.0	56.0	56.0		2821	-6.4	0.0	7	dbSNP_131	56	532,7648		14,504,3572	yes	missense	ABCA13	NM_152701.3	32	14,549,5355	CC,CG,GG		6.5037,1.2309,4.875	benign	941/5059	48312084	577,11259	1828	4090	5918	SO:0001583	missense	154664	exon17			CAAGAAGTTGATA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.2821G>C	7.37:g.48312084G>C	ENSP00000411096:p.Val941Leu	164.0	0.0	0		120.0	26.0	0.216667	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	37	0.048812664907651716	G	4.662	0.123148	0.08931	0.012309	0.065037	ENSG00000179869	ENST00000435803	D	0.82984	-1.67	5.81	-6.43	0.01926	.	1.110050	0.06993	N	0.821921	T	0.09202	0.0227	N	0.16368	0.405	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45775	-0.9238	10	0.05525	T	0.97	.	1.2609	0.02001	0.3788:0.2867:0.186:0.1485	.	941	Q86UQ4	ABCAD_HUMAN	L	941	ENSP00000411096:V941L	ENSP00000411096:V941L	V	+	1	0	ABCA13	48282630	0.000000	0.05858	0.000000	0.03702	0.986000	0.74619	-1.314000	0.02715	-0.919000	0.03803	0.655000	0.94253	GTT	G|0.974;C|0.026	0.026	strong		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
SGK1	6446	hgsc.bcm.edu	37	6	134495154	134495154	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495154G>A	ENST00000237305.7	-	3	305	c.217C>T	c.(217-219)Cct>Tct	p.P73S	SGK1_ENST00000528577.1_Missense_Mutation_p.P101S|SGK1_ENST00000413996.3_Missense_Mutation_p.P87S|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.P63S|SGK1_ENST00000475719.2_Missense_Mutation_p.P73S|SGK1_ENST00000367858.5_Missense_Mutation_p.P168S	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	73					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.P73S(2)|p.P168S(2)|p.P63S(1)|p.P101S(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GGAGGAGAAGGGTTGGCATTC	0.438																																					p.P168S		Atlas-SNP	.											SGK1_ENST00000367858,NS,carcinoma,0,5	SGK1	387	5	6	Substitution - Missense(6)	lung(4)|haematopoietic_and_lymphoid_tissue(2)	c.C502T						PASS	.						150.0	145.0	147.0					6																	134495154		2203	4300	6503	SO:0001583	missense	6446	exon5			GAGAAGGGTTGGC	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.217C>T	6.37:g.134495154G>A	ENSP00000237305:p.Pro73Ser	75.0	0.0	0		60.0	12.0	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799278	0.50208	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.73258	-0.73;-0.7;-0.68;-0.65;-0.7;-0.66	5.99	5.99	0.97316	Protein kinase-like domain (1);	0.047776	0.85682	D	0.000000	T	0.35566	0.0936	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B	0.11329	0.002;0.001;0.001;0.002;0.006;0.0	T	0.28170	-1.0052	10	0.11485	T	0.65	.	13.6422	0.62257	0.0702:0.0:0.9298:0.0	.	101;87;73;63;168;73	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	S	168;87;73;63;101;73;137	ENSP00000356832:P168S;ENSP00000396242:P87S;ENSP00000237305:P73S;ENSP00000356831:P63S;ENSP00000434450:P101S;ENSP00000434302:P73S	ENSP00000237305:P73S	P	-	1	0	SGK1	134536847	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.350000	0.73017	2.840000	0.97914	0.655000	0.94253	CCT	.	.	none		0.438	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
CHD1	1105	hgsc.bcm.edu	37	5	98216991	98216991	+	Nonsense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:98216991C>A	ENST00000284049.3	-	20	3105	c.2956G>T	c.(2956-2958)Gag>Tag	p.E986*		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	986					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ACCTGGGGCTCTTGTTCTTCT	0.318																																					p.E986X		Atlas-SNP	.											.	CHD1	137	.	0			c.G2956T						PASS	.						15.0	14.0	14.0					5																	98216991		2172	4267	6439	SO:0001587	stop_gained	1105	exon20			GGGGCTCTTGTTC	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.2956G>T	5.37:g.98216991C>A	ENSP00000284049:p.Glu986*	197.0	0.0	0		183.0	40.0	0.218579	NM_001270	Q17RZ3	Nonsense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	41	8.840979	0.98974	.	.	ENSG00000153922	ENST00000284049	.	.	.	5.23	5.23	0.72850	.	0.000000	0.33916	U	0.004434	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.1612	0.93533	0.0:1.0:0.0:0.0	.	.	.	.	X	986	.	ENSP00000284049:E986X	E	-	1	0	CHD1	98244891	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.818000	0.86416	2.600000	0.87896	0.585000	0.79938	GAG	.	.	none		0.318	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
TMEM219	124446	hgsc.bcm.edu	37	16	29979376	29979376	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:29979376C>T	ENST00000566848.1	+	3	853	c.386C>T	c.(385-387)aCa>aTa	p.T129I	TMEM219_ENST00000561899.2_Missense_Mutation_p.T129I|TMEM219_ENST00000414689.2_Missense_Mutation_p.T129I|TMEM219_ENST00000279396.6_Missense_Mutation_p.T129I			Q86XT9	TM219_HUMAN	transmembrane protein 219	129					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(1)|prostate(2)	4						GTCCTTATCACAGCCAGGGTG	0.517																																					p.T129I		Atlas-SNP	.											.	TMEM219	10	.	0			c.C386T						PASS	.						99.0	106.0	104.0					16																	29979376		1915	4121	6036	SO:0001583	missense	124446	exon4			TTATCACAGCCAG		CCDS42145.1	16p11.2	2008-08-08			ENSG00000149932	ENSG00000149932			25201	protein-coding gene	gene with protein product							Standard	NM_194280		Approved		uc010bzk.1	Q86XT9		ENST00000566848.1:c.386C>T	16.37:g.29979376C>T	ENSP00000457492:p.Thr129Ile	99.0	0.0	0		95.0	7.0	0.0736842	NM_001083613	D5FK14|Q8WVV8	Missense_Mutation	SNP	ENST00000566848.1	37	CCDS42145.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806497	0.70682	.	.	ENSG00000149932	ENST00000414689;ENST00000279396	.	.	.	5.66	4.65	0.58169	.	0.000000	0.64402	D	0.000002	T	0.58235	0.2108	L	0.29908	0.895	0.36632	D	0.876375	D	0.76494	0.999	D	0.68192	0.956	T	0.65932	-0.6048	9	0.87932	D	0	-17.3834	11.7475	0.51828	0.0:0.8228:0.1772:0.0	.	129	Q86XT9	TM219_HUMAN	I	129	.	ENSP00000279396:T129I	T	+	2	0	TMEM219	29886877	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	2.099000	0.41767	2.665000	0.90641	0.561000	0.74099	ACA	.	.	none		0.517	TMEM219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435307.1	NM_001083613	
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I219V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATTCGCTCCATCTTTGGAAA	0.368		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145.0	129.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1.0	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	2203	4300	6503	SO:0001583	missense	4292	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CGCTCCATCTTTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	81.0	0.0	0		73.0	38.0	0.520548	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
CHMP5	51510	hgsc.bcm.edu	37	9	33266075	33266075	+	Missense_Mutation	SNP	A	A	C	rs146626883	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33266075A>C	ENST00000223500.8	+	2	274	c.137A>C	c.(136-138)aAg>aCg	p.K46T	BAG1_ENST00000379704.2_5'Flank|CHMP5_ENST00000419016.2_Missense_Mutation_p.K46T|BAG1_ENST00000472232.3_5'Flank	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	46					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			GTGAAGTATAAGGATCAGATC	0.448																																					p.K46T		Atlas-SNP	.											CHMP5,rectum,carcinoma,-1,1	CHMP5	15	1	0			c.A137C						PASS	.	A	THR/LYS,THR/LYS	0,4406		0,0,2203	84.0	77.0	79.0		137,137	5.6	1.0	9	dbSNP_134	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CHMP5	NM_001195536.1,NM_016410.5	78,78	0,3,6500	CC,CA,AA		0.0349,0.0,0.0231	probably-damaging,probably-damaging	46/172,46/220	33266075	3,13003	2203	4300	6503	SO:0001583	missense	51510	exon2			AGTATAAGGATCA	AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"""Charged multivesicular body proteins"""	26942	protein-coding gene	gene with protein product		610900	"""chromosome 9 open reading frame 83"", ""chromatin modifying protein 5"""	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765	ENST00000223500.8:c.137A>C	9.37:g.33266075A>C	ENSP00000223500:p.Lys46Thr	72.0	0.0	0		73.0	29.0	0.39726	NM_016410	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	37	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.994287	0.93167	0.0	3.49E-4	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.72725	-0.68;-0.68	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.86318	0.5904	M	0.90922	3.16	0.58432	D	0.999996	D;P	0.67145	0.996;0.933	D;P	0.68353	0.957;0.891	D	0.89316	0.3636	10	0.87932	D	0	-2.8598	13.6556	0.62336	1.0:0.0:0.0:0.0	.	46;46	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	T	46	ENSP00000223500:K46T;ENSP00000442725:K46T	ENSP00000223500:K46T	K	+	2	0	CHMP5	33256075	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.852000	0.92215	2.109000	0.64355	0.379000	0.24179	AAG	A|0.999;C|0.001	0.001	strong		0.448	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410	
MMP24	10893	hgsc.bcm.edu	37	20	33842284	33842284	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:33842284C>A	ENST00000246186.6	+	4	629	c.544C>A	c.(544-546)Cta>Ata	p.L182I	MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000433764.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	182					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	AGTGGGTGAGCTAGACACGCG	0.493																																					p.L182I		Atlas-SNP	.											.	MMP24	35	.	0			c.C544A						PASS	.						180.0	179.0	179.0					20																	33842284		2001	4179	6180	SO:0001583	missense	10893	exon4			GGTGAGCTAGACA	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"""membrane-type 5 matrix metalloproteinase"""	604871	"""matrix metalloproteinase 24 (membrane-inserted)"""			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.544C>A	20.37:g.33842284C>A	ENSP00000246186:p.Leu182Ile	72.0	0.0	0		57.0	15.0	0.263158	NM_006690	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	37	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843928	0.32606	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.21031	2.03	5.53	4.59	0.56863	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.207502	0.41605	D	0.000843	T	0.11024	0.0269	N	0.11560	0.145	0.36654	D	0.877557	B	0.06786	0.001	B	0.12837	0.008	T	0.17623	-1.0363	10	0.24483	T	0.36	.	10.288	0.43579	0.1343:0.7942:0.0:0.0714	.	182	Q9Y5R2	MMP24_HUMAN	I	182;130	ENSP00000246186:L182I	ENSP00000246186:L182I	L	+	1	2	MMP24	33305700	0.998000	0.40836	0.997000	0.53966	0.910000	0.53928	0.975000	0.29449	1.580000	0.49851	0.655000	0.94253	CTA	.	.	none		0.493	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690	
GALNTL6	442117	hgsc.bcm.edu	37	4	173269737	173269737	+	Silent	SNP	T	T	C	rs114177519	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:173269737T>C	ENST00000506823.1	+	5	1107	c.450T>C	c.(448-450)aaT>aaC	p.N150N	GALNTL6_ENST00000457021.1_3'UTR|GALNTL6_ENST00000508122.1_Silent_p.N133N	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	150	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						CATTTCATAATGAAGGTTGGA	0.423													T|||	21	0.00419329	0.0008	0.0086	5008	,	,		19203	0.0		0.0139	False		,,,				2504	0.0				p.N150N		Atlas-SNP	.											.	GALNTL6	102	.	0			c.T450C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	144.0	135.0	138.0		450	-1.7	1.0	4	dbSNP_132	138	62,8538	37.8+/-93.5	0,62,4238	no	coding-synonymous	GALNTL6	NM_001034845.2		0,65,6438	CC,CT,TT		0.7209,0.0681,0.4998		150/602	173269737	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon5			TCATAATGAAGGT		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.450T>C	4.37:g.173269737T>C		111.0	0.0	0		148.0	78.0	0.527027	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			T|0.994;C|0.006	0.006	strong		0.423	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11008594A>T	ENST00000377008.4	-	11	1543	c.1097T>A	c.(1096-1098)gTc>gAc	p.V366D	C1orf127_ENST00000377004.4_Missense_Mutation_p.V533D			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	366			V -> D (in dbSNP:rs1281016).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGTCCTGAGACCAGAAGTGA	0.612													A|||	346	0.0690895	0.2035	0.0144	5008	,	,		19200	0.004		0.0427	False		,,,				2504	0.0204				p.V533D		Atlas-SNP	.											.	C1orf127	134	.	0			c.T1598A						PASS	.	A	ASP/VAL	735,3671	303.5+/-288.0	65,605,1533	56.0	53.0	54.0		1598	0.5	0.0	1	dbSNP_87	54	343,8257	116.3+/-176.0	4,335,3961	yes	missense	C1orf127	NM_001170754.1	152	69,940,5494	TT,TA,AA		3.9884,16.6818,8.2885	probably-damaging	533/824	11008594	1078,11928	2203	4300	6503	SO:0001583	missense	148345	exon12			CCTGAGACCAGAA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1097T>A	1.37:g.11008594A>T	ENSP00000366207:p.Val366Asp	126.0	0.0	0		159.0	83.0	0.522013	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	A|A	13.05|13.05	2.122259|2.122259	0.37436|0.37436	0.166818|0.166818	0.039884|0.039884	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.26518	.|1.73;1.73	4.15|4.15	0.48|0.48	0.16804|0.16804	.|.	.|0.956786	.|0.08574	.|N	.|0.925628	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|P;P;P	.|0.46512	.|0.879;0.879;0.879	.|B;B;B	.|0.42163	.|0.378;0.378;0.378	T|T	0.19484|0.19484	-1.0304|-1.0304	4|9	.|0.15952	.|T	.|0.53	-5.9143|-5.9143	0.8883|0.8883	0.01249|0.01249	0.3866:0.3152:0.136:0.1622|0.3866:0.3152:0.136:0.1622	rs1281016;rs52819154;rs1281016|rs1281016;rs52819154;rs1281016	.|384;358;366	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	T|D	368;485|533;366	.|ENSP00000366203:V533D;ENSP00000366207:V366D	.|ENSP00000366203:V533D	S|V	-|-	1|2	0|0	C1orf127|C1orf127	10931181|10931181	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.057000|0.057000	0.15508|0.15508	-0.110000|-0.110000	0.10824|0.10824	0.317000|0.317000	0.23160|0.23160	0.402000|0.402000	0.26972|0.26972	TCT|GTC	A|0.922;T|0.078	0.078	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
ABCG8	64241	hgsc.bcm.edu	37	2	44073405	44073405	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44073405T>C	ENST00000272286.2	+	3	367	c.277T>C	c.(277-279)Ttc>Ctc	p.F93L		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	93	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	GAACCTAAGCTTCAAAGTGAG	0.532																																					p.F93L		Atlas-SNP	.											.	ABCG8	98	.	0			c.T277C						PASS	.						72.0	68.0	69.0					2																	44073405		2203	4300	6503	SO:0001583	missense	64241	exon3			CTAAGCTTCAAAG	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.277T>C	2.37:g.44073405T>C	ENSP00000272286:p.Phe93Leu	115.0	0.0	0		109.0	26.0	0.238532	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	.	.	.	.	.	.	.	.	.	.	T	0.949	-0.707002	0.03230	.	.	ENSG00000143921	ENST00000272286	D	0.92805	-3.11	5.69	4.34	0.51931	ABC transporter-like (1);	0.256767	0.41712	N	0.000831	T	0.80586	0.4651	N	0.16602	0.42	0.37015	D	0.895938	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.72381	-0.4311	10	0.02654	T	1	.	7.4098	0.27011	0.0:0.1238:0.134:0.7422	.	93;93	Q9H221-2;Q9H221	.;ABCG8_HUMAN	L	93	ENSP00000272286:F93L	ENSP00000272286:F93L	F	+	1	0	ABCG8	43926909	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	2.243000	0.43115	2.168000	0.68352	0.528000	0.53228	TTC	.	.	none		0.532	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
AKAP8L	26993	hgsc.bcm.edu	37	19	15491357	15491357	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15491357T>C	ENST00000397410.5	-	13	1733	c.1603A>G	c.(1603-1605)Atc>Gtc	p.I535V	AKAP8L_ENST00000595465.2_Missense_Mutation_p.I474V|AKAP8_ENST00000269701.2_5'Flank|AC005785.2_ENST00000597164.2_RNA	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	535						cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(4)|kidney(2)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						TTCTTGCTGATGAGCTTGTTG	0.617																																					p.I535V		Atlas-SNP	.											.	AKAP8L	64	.	0			c.A1603G						PASS	.						62.0	69.0	67.0					19																	15491357		2040	4188	6228	SO:0001583	missense	26993	exon13			TGCTGATGAGCTT	BC000713	CCDS46005.1	19p13.12	2013-10-16			ENSG00000011243	ENSG00000011243			29857	protein-coding gene	gene with protein product	"""neighbor of A kinase anchoring protein 95"""	609475				10748171, 10761695	Standard	XM_005259854		Approved	NAKAP95, HAP95	uc002naw.1	Q9ULX6	OTTHUMG00000182446	ENST00000397410.5:c.1603A>G	19.37:g.15491357T>C	ENSP00000380557:p.Ile535Val	98.0	0.0	0		93.0	48.0	0.516129	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Missense_Mutation	SNP	ENST00000397410.5	37	CCDS46005.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096921	0.76870	.	.	ENSG00000011243	ENST00000397410	T	0.43294	0.95	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	N	0.25890	0.77	0.42859	D	0.994105	P;P	0.47604	0.898;0.898	D;D	0.68192	0.956;0.956	T	0.49606	-0.8922	10	0.45353	T	0.12	-15.6199	12.1116	0.53842	0.0:0.0:0.0:1.0	.	474;535	B4DJ74;Q9ULX6	.;AKP8L_HUMAN	V	535	ENSP00000380557:I535V	ENSP00000380557:I535V	I	-	1	0	AKAP8L	15352357	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.505000	0.60421	1.854000	0.53819	0.459000	0.35465	ATC	.	.	none		0.617	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371	
C17orf74	201243	hgsc.bcm.edu	37	17	7330307	7330307	+	Missense_Mutation	SNP	C	C	T	rs146528431	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7330307C>T	ENST00000333870.3	+	3	1071	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	333						integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				CCGGAACGCCCGGCCTGAGGC	0.692													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		14183	0.0		0.0099	False		,,,				2504	0.001				p.R333W		Atlas-SNP	.											.	C17orf74	56	.	0			c.C997T						PASS	.	C	TRP/ARG	6,3938		0,6,1966	17.0	21.0	20.0		997	1.3	0.0	17	dbSNP_134	20	69,8203		0,69,4067	no	missense	C17orf74	NM_175734.4	101	0,75,6033	TT,TC,CC		0.8341,0.1521,0.6139	probably-damaging	333/502	7330307	75,12141	1972	4136	6108	SO:0001583	missense	201243	exon3			AACGCCCGGCCTG	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.997C>T	17.37:g.7330307C>T	ENSP00000328061:p.Arg333Trp	77.0	0.0	0		61.0	41.0	0.672131	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	14	0.00641025641025641	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	4.791	0.147015	0.09134	0.001521	0.008341	ENSG00000184560	ENST00000333870	T	0.37058	1.22	4.59	1.29	0.21616	.	0.000000	0.34828	N	0.003652	T	0.16896	0.0406	L	0.32530	0.975	0.09310	N	1	B	0.15719	0.014	B	0.06405	0.002	T	0.16394	-1.0404	10	0.87932	D	0	-6.0266	5.6303	0.17506	0.355:0.5485:0.0:0.0964	.	333	Q0P670	CQ074_HUMAN	W	333	ENSP00000328061:R333W	ENSP00000328061:R333W	R	+	1	2	C17orf74	7271031	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.278000	0.08490	0.091000	0.17302	-0.320000	0.08662	CGG	C|0.995;T|0.005	0.005	strong		0.692	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
PTPN3	5774	hgsc.bcm.edu	37	9	112145817	112145817	+	Silent	SNP	C	C	T	rs146869100		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:112145817C>T	ENST00000374541.2	-	23	2372	c.2268G>A	c.(2266-2268)caG>caA	p.Q756Q	PTPN3_ENST00000446349.1_Silent_p.Q580Q|PTPN3_ENST00000412145.1_Silent_p.Q625Q|PTPN3_ENST00000262539.3_Silent_p.Q602Q|PTPN3_ENST00000394827.3_Silent_p.Q224Q	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	756	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CTGGCCAGTACTGGTGACATT	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		17585	0.0		0.001	False		,,,				2504	0.0				p.Q756Q		Atlas-SNP	.											.	PTPN3	106	.	0			c.G2268A						PASS	.	C	,,,,,	3,4403	6.2+/-15.9	0,3,2200	121.0	113.0	116.0		2133,1875,1740,1407,1272,2268	4.8	1.0	9	dbSNP_134	116	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	0,21,6482	TT,TC,CC		0.2093,0.0681,0.1615	,,,,,	711/869,625/783,580/738,469/627,424/582,756/914	112145817	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon23			CCAGTACTGGTGA		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2268G>A	9.37:g.112145817C>T		82.0	0.0	0		79.0	41.0	0.518987	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
ZP3	7784	hgsc.bcm.edu	37	7	76062798	76062798	+	Missense_Mutation	SNP	G	G	A	rs74676082	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76062798G>A	ENST00000394857.3	+	4	605	c.547G>A	c.(547-549)Gct>Act	p.A183T	ZP3_ENST00000336517.4_Missense_Mutation_p.A132T|ZP3_ENST00000416245.1_Missense_Mutation_p.A7T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	183	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GAACTGGAACGCTGAGAAGAG	0.592													G|||	33	0.00658946	0.0008	0.0418	5008	,	,		18285	0.0		0.003	False		,,,				2504	0.0				p.A183T		Atlas-SNP	.											.	ZP3	32	.	0			c.G547A						PASS	.	G	THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	72.0	69.0	70.0		547,394	-10.8	0.0	7	dbSNP_131	70	49,8551	31.2+/-83.2	0,49,4251	yes	missense,missense	ZP3	NM_001110354.1,NM_007155.5	58,58	0,51,6452	AA,AG,GG		0.5698,0.0454,0.3921	benign,benign	183/425,132/374	76062798	51,12955	2203	4300	6503	SO:0001583	missense	7784	exon4			TGGAACGCTGAGA	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.547G>A	7.37:g.76062798G>A	ENSP00000378326:p.Ala183Thr	39.0	0.0	0		21.0	13.0	0.619048	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	13	0.005952380952380952	0	0.0	10	0.027624309392265192	0	0.0	3	0.00395778364116095	G	0.623	-0.820170	0.02755	4.54E-4	0.005698	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.81247	-1.47;-1.47;-1.47	5.4	-10.8	0.00216	Zona pellucida sperm-binding protein (3);	1.021960	0.07766	N	0.950871	T	0.23289	0.0563	N	0.05177	-0.1	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.21245	-1.0251	10	0.07030	T	0.85	0.1179	3.818	0.08824	0.5092:0.0732:0.1109:0.3067	.	132;183	P21754-3;P21754	.;ZP3_HUMAN	T	132;183;183;7	ENSP00000337310:A132T;ENSP00000378326:A183T;ENSP00000411955:A7T	ENSP00000337310:A132T	A	+	1	0	ZP3	75900734	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-2.663000	0.00849	-3.205000	0.00216	-1.069000	0.02264	GCT	G|0.996;A|0.004	0.004	strong		0.592	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
PUS3	83480	hgsc.bcm.edu	37	11	125764156	125764156	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125764156A>C	ENST00000530811.1	-	3	1015	c.970T>G	c.(970-972)Tta>Gta	p.L324V	HYLS1_ENST00000425380.2_Intron|PUS3_ENST00000227474.3_Missense_Mutation_p.L324V|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	324					tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		CAGTCATATAAGACTAGAGGA	0.363																																					p.L324V		Atlas-SNP	.											.	PUS3	33	.	0			c.T970G						PASS	.						56.0	62.0	60.0					11																	125764156		2200	4295	6495	SO:0001583	missense	83480	exon4			CATATAAGACTAG	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.970T>G	11.37:g.125764156A>C	ENSP00000432386:p.Leu324Val	33.0	0.0	0		62.0	8.0	0.129032	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745579	0.69418	.	.	ENSG00000110060	ENST00000227474;ENST00000530811	T;T	0.75050	-0.9;-0.9	5.64	1.72	0.24424	Pseudouridine synthase I, TruA, C-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.000000	0.85682	D	0.000000	D	0.87869	0.6286	H	0.96518	3.835	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.85879	0.1421	10	0.87932	D	0	-8.6407	6.4206	0.21742	0.4951:0.0:0.5049:0.0	.	324	Q9BZE2	PUS3_HUMAN	V	324	ENSP00000227474:L324V;ENSP00000432386:L324V	ENSP00000227474:L324V	L	-	1	2	PUS3	125269366	1.000000	0.71417	0.927000	0.36925	0.980000	0.70556	3.443000	0.52907	0.507000	0.28148	0.482000	0.46254	TTA	.	.	none		0.363	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
TENM1	10178	hgsc.bcm.edu	37	X	123539063	123539063	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:123539063A>C	ENST00000371130.3	-	26	5251	c.5188T>G	c.(5188-5190)Ttt>Gtt	p.F1730V	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.F1737V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1730					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCGCTGGCAAAAGTGACACGC	0.547																																					p.F1737V		Atlas-SNP	.											.	.	.	.	0			c.T5209G						PASS	.						82.0	68.0	73.0					X																	123539063		2203	4300	6503	SO:0001583	missense	10178	exon27			TGGCAAAAGTGAC	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5188T>G	X.37:g.123539063A>C	ENSP00000360171:p.Phe1730Val	39.0	0.0	0		60.0	25.0	0.416667	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.855583	0.51376	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85013	-1.93;-1.89	5.56	5.56	0.83823	.	0.188786	0.47093	D	0.000251	T	0.79203	0.4406	L	0.40543	1.245	0.42964	D	0.99441	B;B;B	0.24483	0.104;0.049;0.059	B;B;B	0.19148	0.024;0.024;0.021	T	0.74612	-0.3607	10	0.23302	T	0.38	.	14.742	0.69464	1.0:0.0:0.0:0.0	.	1736;1737;1730	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	1730;1737	ENSP00000360171:F1730V;ENSP00000403954:F1737V	ENSP00000360171:F1730V	F	-	1	0	ODZ1	123366744	1.000000	0.71417	0.958000	0.39756	0.887000	0.51463	5.898000	0.69838	1.862000	0.54008	0.486000	0.48141	TTT	.	.	none		0.547	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
FLG	2312	hgsc.bcm.edu	37	1	152275921	152275921	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152275921C>T	ENST00000368799.1	-	3	11476	c.11441G>A	c.(11440-11442)cGt>cAt	p.R3814H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3814	Ser-rich.		R -> C (in dbSNP:rs2184953).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R3814H(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCTCATTACGTGTTTCTCT	0.577									Ichthyosis																												p.R3814H		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - Missense(1)	lung(1)	c.G11441A						PASS	.						377.0	368.0	371.0					1																	152275921		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCATTACGTGTTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11441G>A	1.37:g.152275921C>T	ENSP00000357789:p.Arg3814His	161.0	0.0	0		156.0	57.0	0.365385	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	9.179	1.023218	0.19433	.	.	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.47	0.363	0.16118	.	.	.	.	.	T	0.01454	0.0047	L	0.31207	0.915	0.09310	N	1	D	0.71674	0.998	D	0.69479	0.964	T	0.53027	-0.8496	9	0.35671	T	0.21	.	8.2839	0.31917	0.0:0.5204:0.4796:0.0	.	3814	P20930	FILA_HUMAN	H	3814	ENSP00000357789:R3814H	ENSP00000357789:R3814H	R	-	2	0	FLG	150542545	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.512000	0.00446	-0.036000	0.13669	-0.369000	0.07265	CGT	.	.	none		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MT-ND4	4538	hgsc.bcm.edu	37	M	11044	11044	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrM:11044C>T	ENST00000361381.2	+	1	285	c.285C>T	c.(283-285)taC>taT	p.Y95Y	MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	95					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AAAAAACTCTACCTCTCTATA	0.413																																					p.Y95Y		Atlas-SNP	.											.	.	.	.	0			c.C285T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTCTACCTCTCT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.285C>T	M.37:g.11044C>T		10.0	0.0	0		6.0	6.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.413	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SSC5D	284297	hgsc.bcm.edu	37	19	56011279	56011279	+	Missense_Mutation	SNP	C	C	T	rs35651406	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56011279C>T	ENST00000389623.6	+	10	1825	c.1802C>T	c.(1801-1803)gCc>gTc	p.A601V	SSC5D_ENST00000587166.1_Missense_Mutation_p.A601V	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	601					defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						GGAGAGCTGGCCACCAAGCCC	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		15740	0.0		0.003	False		,,,				2504	0.0				p.A601V		Atlas-SNP	.											.	SSC5D	65	.	0			c.C1802T						PASS	.	C	VAL/ALA,VAL/ALA	1,1383		0,1,691	84.0	89.0	88.0		1802,1802	-3.0	0.0	19	dbSNP_126	88	25,3157		0,25,1566	yes	missense,missense	SSC5D	NM_001144950.1,NM_001195267.1	64,64	0,26,2257	TT,TC,CC		0.7857,0.0723,0.5694	benign,benign	601/1574,601/952	56011279	26,4540	692	1591	2283	SO:0001583	missense	284297	exon10			AGCTGGCCACCAA		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.1802C>T	19.37:g.56011279C>T	ENSP00000374274:p.Ala601Val	40.0	0.0	0		48.0	26.0	0.541667	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	11.31	1.600743	0.28534	7.23E-4	0.007857	ENSG00000179954	ENST00000389623;ENST00000541230	T	0.01527	4.8	5.04	-2.96	0.05547	.	.	.	.	.	T	0.00845	0.0028	N	0.24115	0.695	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.48340	-0.9044	9	0.15066	T	0.55	.	5.4295	0.16446	0.0:0.4191:0.138:0.4429	rs35651406	601	A1L4H1	SRCRL_HUMAN	V	601	ENSP00000374274:A601V	ENSP00000374274:A601V	A	+	2	0	SSC5D	60703091	0.000000	0.05858	0.025000	0.17156	0.487000	0.33371	-0.562000	0.05950	-0.598000	0.05806	-1.330000	0.01273	GCC	C|0.997;T|0.003	0.003	strong		0.587	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
DTNB	1838	hgsc.bcm.edu	37	2	25611102	25611102	+	Silent	SNP	G	G	A	rs200383554	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:25611102G>A	ENST00000406818.3	-	17	1953	c.1704C>T	c.(1702-1704)gtC>gtT	p.V568V	DTNB_ENST00000496972.2_Silent_p.V504V|DTNB_ENST00000405222.1_Silent_p.V531V|DTNB_ENST00000404103.3_Silent_p.V568V|DTNB_ENST00000545439.1_Silent_p.V357V|DTNB_ENST00000407186.1_Silent_p.V531V|DTNB_ENST00000407661.3_Silent_p.V568V|DTNB_ENST00000407038.3_Silent_p.V538V|DTNB_ENST00000288642.8_Silent_p.V568V	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	568						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTCTCCCCCGACTCCGCTCA	0.652													G|||	4	0.000798722	0.0008	0.0	5008	,	,		16368	0.0		0.002	False		,,,				2504	0.001				p.V568V		Atlas-SNP	.											.	DTNB	43	.	0			c.C1704T						PASS	.	G	,,,,	5,3975		0,5,1985	18.0	22.0	21.0		1704,1704,1614,1704,1593	-3.3	0.5	2		21	42,8304		0,42,4131	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	,,,,	0,47,6116	AA,AG,GG		0.5032,0.1256,0.3813	,,,,	568/628,568/598,538/568,568/610,531/561	25611102	47,12279	1990	4173	6163	SO:0001819	synonymous_variant	1838	exon17			TCCCCCGACTCCG	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1704C>T	2.37:g.25611102G>A		45.0	0.0	0		36.0	22.0	0.611111	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																			G|1.000;A|0.000	0.000	strong		0.652	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
LIG4	3981	hgsc.bcm.edu	37	13	108862810	108862810	+	Silent	SNP	G	G	A	rs2232638	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:108862810G>A	ENST00000356922.4	-	2	1079	c.807C>T	c.(805-807)taC>taT	p.Y269Y	LIG4_ENST00000442234.1_Silent_p.Y269Y|LIG4_ENST00000405925.1_Silent_p.Y269Y	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	269					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TGGTTTCTATGTAGAAACTCT	0.343								Non-homologous end-joining					G|||	177	0.0353435	0.1263	0.0144	5008	,	,		21707	0.0		0.0	False		,,,				2504	0.0				p.Y269Y		Atlas-SNP	.											.	LIG4	91	.	0			c.C807T						PASS	.	G	,,	443,3963	204.5+/-226.7	28,387,1788	68.0	66.0	67.0		807,807,807	4.7	1.0	13	dbSNP_98	67	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	,,	28,391,6083	AA,AG,GG		0.0465,10.0545,3.4374	,,	269/912,269/912,269/912	108862810	447,12557	2203	4299	6502	SO:0001819	synonymous_variant	3981	exon3			TTCTATGTAGAAA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.807C>T	13.37:g.108862810G>A		103.0	0.0	0		72.0	14.0	0.194444	NM_206937	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																			G|0.956;A|0.044	0.044	strong		0.343	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
ZP3	7784	hgsc.bcm.edu	37	7	76062913	76062913	+	Missense_Mutation	SNP	C	C	G	rs139729790	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76062913C>G	ENST00000394857.3	+	4	720	c.662C>G	c.(661-663)cCg>cGg	p.P221R	ZP3_ENST00000336517.4_Missense_Mutation_p.P170R|ZP3_ENST00000416245.1_Missense_Mutation_p.P45R	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	221	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GTGGCCACACCGACACCAGAC	0.592													C|||	22	0.00439297	0.0015	0.0058	5008	,	,		19217	0.0		0.0119	False		,,,				2504	0.0041				p.P221R		Atlas-SNP	.											ZP3_ENST00000394857,NS,lymphoid_neoplasm,0,2	ZP3	32	2	0			c.C662G						PASS	.	C	ARG/PRO,ARG/PRO	18,4388	25.3+/-52.1	0,18,2185	132.0	113.0	119.0		662,509	-2.1	0.0	7	dbSNP_134	119	119,8481	62.4+/-124.4	0,119,4181	yes	missense,missense	ZP3	NM_001110354.1,NM_007155.5	103,103	0,137,6366	GG,GC,CC		1.3837,0.4085,1.0534	probably-damaging,probably-damaging	221/425,170/374	76062913	137,12869	2203	4300	6503	SO:0001583	missense	7784	exon4			CCACACCGACACC	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.662C>G	7.37:g.76062913C>G	ENSP00000378326:p.Pro221Arg	74.0	0.0	0		59.0	26.0	0.440678	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	9.849|9.849	1.193169|1.193169	0.22037|0.22037	0.004085|0.004085	0.013837|0.013837	ENSG00000188372|ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245|ENST00000394860	D;D;D|.	0.83837|.	-1.77;-1.77;-1.77|.	5.42|5.42	-2.08|-2.08	0.07254|0.07254	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);|.	1.140650|.	0.06482|.	N|.	0.733073|.	T|T	0.32133|0.32133	0.0819|0.0819	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	D;D|.	0.69078|.	0.997;0.991|.	D;D|.	0.70487|.	0.969;0.951|.	T|T	0.39522|0.39522	-0.9610|-0.9610	10|5	0.39692|.	T|.	0.17|.	-8.2099|-8.2099	6.7596|6.7596	0.23532|0.23532	0.1157:0.4103:0.0:0.474|0.1157:0.4103:0.0:0.474	.|.	170;221|.	P21754-3;P21754|.	.;ZP3_HUMAN|.	R|G	170;221;221;45|43	ENSP00000337310:P170R;ENSP00000378326:P221R;ENSP00000411955:P45R|.	ENSP00000337310:P170R|.	P|R	+|+	2|1	0|2	ZP3|ZP3	75900849|75900849	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	0.066000|0.066000	0.14489|0.14489	-0.288000|-0.288000	0.09051|0.09051	-0.768000|-0.768000	0.03414|0.03414	CCG|CGA	C|0.991;G|0.009	0.009	strong		0.592	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
JAK1	3716	hgsc.bcm.edu	37	1	65312343	65312343	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:65312343C>T	ENST00000342505.4	-	14	2224	c.1976G>A	c.(1975-1977)cGc>cAc	p.R659H	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	659	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTCCACGTCGCGGACACAGAC	0.582			Mis		ALL																																p.R659H		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,malignant_melanoma,0,1	JAK1	209	1	0			c.G1976A						PASS	.						83.0	90.0	88.0					1																	65312343		2141	4271	6412	SO:0001583	missense	3716	exon14			ACGTCGCGGACAC	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1976G>A	1.37:g.65312343C>T	ENSP00000343204:p.Arg659His	94.0	0.0	0		73.0	20.0	0.273973	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	8.986	0.976479	0.18736	.	.	ENSG00000162434	ENST00000342505	D	0.82803	-1.65	4.3	3.39	0.38822	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.60011	0.2236	L	0.45422	1.42	0.43457	D	0.995651	B	0.30973	0.302	B	0.24006	0.05	T	0.59925	-0.7362	9	0.13470	T	0.59	-3.1424	12.914	0.58195	0.0:0.9197:0.0:0.0803	.	659	P23458	JAK1_HUMAN	H	659	ENSP00000343204:R659H	ENSP00000343204:R659H	R	-	2	0	JAK1	65084931	0.996000	0.38824	0.930000	0.37139	0.236000	0.25371	3.316000	0.51960	1.395000	0.46643	0.561000	0.74099	CGC	.	.	none		0.582	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
PTPN12	5782	hgsc.bcm.edu	37	7	77267956	77267956	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:77267956G>A	ENST00000248594.6	+	17	2461	c.2189G>A	c.(2188-2190)gGt>gAt	p.G730D	PTPN12_ENST00000435495.2_Missense_Mutation_p.G600D|PTPN12_ENST00000415482.2_Missense_Mutation_p.G611D	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	730					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CCAGCGGGAGGTATTCACTAT	0.348																																					p.G730D		Atlas-SNP	.											.	PTPN12	83	.	0			c.G2189A						PASS	.						108.0	110.0	109.0					7																	77267956		2203	4300	6503	SO:0001583	missense	5782	exon17			CGGGAGGTATTCA		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.2189G>A	7.37:g.77267956G>A	ENSP00000248594:p.Gly730Asp	128.0	0.0	0		101.0	47.0	0.465347	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	G	4.258	0.046837	0.08243	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000435495;ENST00000407343	T;T;T;T	0.32753	3.88;3.29;3.29;1.44	5.5	1.15	0.20763	.	1.074940	0.07016	N	0.825987	T	0.24392	0.0591	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	10	0.38643	T	0.18	.	4.3593	0.11194	0.2806:0.0:0.5685:0.1509	.	730	Q05209	PTN12_HUMAN	D	730;611;600;212	ENSP00000248594:G730D;ENSP00000392429:G611D;ENSP00000397991:G600D;ENSP00000385079:G212D	ENSP00000248594:G730D	G	+	2	0	PTPN12	77105892	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	0.138000	0.16016	-0.011000	0.14247	0.551000	0.68910	GGT	.	.	none		0.348	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
CYP3A4	1576	hgsc.bcm.edu	37	7	99358604	99358604	+	Splice_Site	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358604T>C	ENST00000336411.2	-	12	1437	c.1254A>G	c.(1252-1254)agA>agG	p.R418R	CYP3A4_ENST00000354593.2_Splice_Site_p.R268R	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	418					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	TCTTGCTGAATCTGGTTCCAC	0.413																																					p.R418R		Atlas-SNP	.											.	CYP3A4	56	.	0			c.A1254G						PASS	.						372.0	324.0	341.0					7																	99358604		2203	4300	6503	SO:0001630	splice_region_variant	1576	exon12			GCTGAATCTGGTT	AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"""Cytochrome P450s"""	2637	protein-coding gene	gene with protein product		124010	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"""	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.1254-1A>G	7.37:g.99358604T>C		270.0	1.0	0.0037037		240.0	102.0	0.425	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1		Silent
ABCA2	20	hgsc.bcm.edu	37	9	139904722	139904722	+	Silent	SNP	C	C	T	rs34125425	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139904722C>T	ENST00000371605.3	-	40	6420	c.6273G>A	c.(6271-6273)gcG>gcA	p.A2091A	ABCA2_ENST00000341511.6_Silent_p.A2092A|ABCA2_ENST00000265662.5_Silent_p.A2092A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2091	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		TGGTCTTGCCCGCACCGTTGA	0.667													C|||	66	0.0131789	0.0008	0.0288	5008	,	,		11162	0.0		0.0278	False		,,,				2504	0.0174				p.A2122A		Atlas-SNP	.											.	ABCA2	113	.	0			c.G6366A						PASS	.	C	,	18,4210		0,18,2096	12.0	15.0	14.0		6276,6366	-6.7	0.4	9	dbSNP_126	14	212,8236		1,210,4013	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	1,228,6109	TT,TC,CC		2.5095,0.4257,1.8145	,	2092/2437,2122/2467	139904722	230,12446	2114	4224	6338	SO:0001819	synonymous_variant	20	exon41			CTTGCCCGCACCG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.6273G>A	9.37:g.139904722C>T		60.0	0.0	0		63.0	30.0	0.47619	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				C|0.984;T|0.016	0.016	strong		0.667	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
P4HA2	8974	hgsc.bcm.edu	37	5	131539462	131539462	+	Silent	SNP	T	T	C	rs144253110	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131539462T>C	ENST00000401867.1	-	11	1798	c.1230A>G	c.(1228-1230)gtA>gtG	p.V410V	P4HA2_ENST00000360568.3_Silent_p.V410V|P4HA2_ENST00000379104.2_Silent_p.V410V|P4HA2_ENST00000166534.4_Silent_p.V410V|P4HA2_ENST00000379100.2_Silent_p.V410V|P4HA2_ENST00000379086.1_Silent_p.V410V			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	410					peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	CTGCAGTCTTTACTGTTAACC	0.493																																					p.V410V	Esophageal Squamous(68;117 1135 17362 19256 34242)	Atlas-SNP	.											.	P4HA2	72	.	0			c.A1230G						PASS	.	T	,,,,	0,4406		0,0,2203	88.0	75.0	80.0		1230,1230,1230,1230,1230	-8.1	0.6	5	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	P4HA2	NM_001017973.1,NM_001017974.1,NM_001142598.1,NM_001142599.1,NM_004199.2	,,,,	0,11,6492	CC,CT,TT		0.1279,0.0,0.0846	,,,,	410/534,410/534,410/534,410/536,410/536	131539462	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	8974	exon10			AGTCTTTACTGTT	U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"""4-PH alpha 2"", ""collagen prolyl 4-hydroxylase alpha(II)"""	600608	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"""			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.1230A>G	5.37:g.131539462T>C		118.0	0.0	0		136.0	64.0	0.470588	NM_001017974	D3DQ85|D3DQ86|Q8WWN0	Silent	SNP	ENST00000401867.1	37	CCDS4151.1																																																																																			T|0.999;C|0.001	0.001	strong		0.493	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199	
LTBP1	4052	hgsc.bcm.edu	37	2	33172827	33172827	+	Missense_Mutation	SNP	G	G	A	rs147166401	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:33172827G>A	ENST00000404816.2	+	1	789	c.436G>A	c.(436-438)Gag>Aag	p.E146K	Y_RNA_ENST00000384224.1_RNA|LTBP1_ENST00000354476.3_Missense_Mutation_p.E146K			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	146					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GGTGCCGCAGGAGACCCAGAG	0.721													G|||	19	0.00379393	0.0	0.0058	5008	,	,		8786	0.0		0.0089	False		,,,				2504	0.0061				p.E146K		Atlas-SNP	.											.	LTBP1	317	.	0			c.G436A						PASS	.	G	LYS/GLU	11,3139		0,11,1564	9.0	9.0	9.0		436	2.6	0.1	2	dbSNP_134	9	94,5748		1,92,2828	yes	missense	LTBP1	NM_206943.2	56	1,103,4392	AA,AG,GG		1.609,0.3492,1.1677	benign	146/1722	33172827	105,8887	1575	2921	4496	SO:0001583	missense	4052	exon1			CCGCAGGAGACCC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.436G>A	2.37:g.33172827G>A	ENSP00000386043:p.Glu146Lys	84.0	0.0	0		67.0	39.0	0.58209	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	13.22	2.172646	0.38413	0.003492	0.01609	ENSG00000049323	ENST00000404816;ENST00000354476	T;T	0.80909	-1.43;-1.41	4.59	2.64	0.31445	.	.	.	.	.	T	0.47728	0.1461	N	0.14661	0.345	0.19575	N	0.999965	B	0.15473	0.013	B	0.19391	0.025	T	0.43032	-0.9416	9	0.25106	T	0.35	.	7.6966	0.28598	0.089:0.2885:0.6225:0.0	.	146	Q14766-4	.	K	146	ENSP00000386043:E146K;ENSP00000346467:E146K	ENSP00000346467:E146K	E	+	1	0	LTBP1	33026331	0.999000	0.42202	0.068000	0.19968	0.979000	0.70002	2.030000	0.41108	0.919000	0.36945	0.561000	0.74099	GAG	G|0.992;A|0.008	0.008	strong		0.721	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
GLRA4	441509	hgsc.bcm.edu	37	X	102974119	102974119	+	Silent	SNP	G	G	A	rs41300882	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:102974119G>A	ENST00000372617.4	-	7	1219	c.799C>T	c.(799-801)Cta>Tta	p.L267L	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	267						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						ACGATGAGTAGGCTGGGGATG	0.557													G|||	11	0.00291391	0.0	0.0014	3775	,	,		14691	0.0		0.007	False		,,,				2504	0.0031				p.L267L		Atlas-SNP	.											.	GLRA4	86	.	0			c.C799T						PASS	.	G	,	8,3827		0,7,1,1625,570	156.0	159.0	158.0		799,799	4.9	1.0	X	dbSNP_127	158	87,6640		1,60,25,2367,1846	no	coding-synonymous,coding-synonymous	GLRA4	NM_001024452.2,NM_001172285.1	,	1,67,26,3992,2416	AA,AG,A,GG,G		1.2933,0.2086,0.8995	,	267/418,267/343	102974119	95,10467	2203	4299	6502	SO:0001819	synonymous_variant	441509	exon7			TGAGTAGGCTGGG	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.799C>T	X.37:g.102974119G>A		128.0	0.0	0		196.0	141.0	0.719388	NM_001024452		Silent	SNP	ENST00000372617.4	37	CCDS43980.2																																																																																			G|0.995;A|0.005	0.005	strong		0.557	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
TUB	7275	hgsc.bcm.edu	37	11	8119298	8119298	+	Missense_Mutation	SNP	A	A	G	rs55892969	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:8119298A>G	ENST00000299506.2	+	8	1072	c.923A>G	c.(922-924)aAa>aGa	p.K308R	TUB_ENST00000305253.4_Missense_Mutation_p.K363R|TUB_ENST00000534099.1_Missense_Mutation_p.K314R	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	308					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		AAGAAGAGTAAAACTTCCAAT	0.517													A|||	40	0.00798722	0.0008	0.0072	5008	,	,		20036	0.0		0.0298	False		,,,				2504	0.0041				p.K363R		Atlas-SNP	.											.	TUB	71	.	0			c.A1088G						PASS	.	A	ARG/LYS,ARG/LYS	31,4371	36.8+/-68.6	0,31,2170	157.0	165.0	162.0		1088,923	4.7	1.0	11	dbSNP_129	162	253,8339	99.9+/-161.4	6,241,4049	yes	missense,missense	TUB	NM_003320.4,NM_177972.2	26,26	6,272,6219	GG,GA,AA		2.9446,0.7042,2.1856	benign,benign	363/562,308/507	8119298	284,12710	2201	4296	6497	SO:0001583	missense	7275	exon9			AGAGTAAAACTTC	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.923A>G	11.37:g.8119298A>G	ENSP00000299506:p.Lys308Arg	112.0	0.0	0		106.0	59.0	0.556604	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	27	0.012362637362637362	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	23	0.030343007915567283	A	20.5	4.002333	0.74932	0.007042	0.029446	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.96619	-4.07;-4.07;-4.07	4.7	4.7	0.59300	Tubby, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89206	0.6649	L	0.55743	1.74	0.80722	D	1	B;B;B	0.32245	0.19;0.361;0.326	B;B;B	0.39503	0.11;0.301;0.297	D	0.90008	0.4119	10	0.56958	D	0.05	-22.229	14.4578	0.67428	1.0:0.0:0.0:0.0	rs55892969	314;308;363	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	R	314;363;308	ENSP00000434400:K314R;ENSP00000305426:K363R;ENSP00000299506:K308R	ENSP00000299506:K308R	K	+	2	0	TUB	8075874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.886000	0.54624	0.477000	0.44152	AAA	A|0.983;G|0.017	0.017	strong		0.517	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
UNC13B	10497	hgsc.bcm.edu	37	9	35399243	35399243	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35399243G>A	ENST00000378495.3	+	33	4135	c.3913G>A	c.(3913-3915)Gag>Aag	p.E1305K	UNC13B_ENST00000396787.1_Missense_Mutation_p.E1317K|UNC13B_ENST00000378496.4_Missense_Mutation_p.E1305K	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1305	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GAACACAATGGAGAGGATGAT	0.562																																					p.E1305K		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3913A						PASS	.						210.0	182.0	192.0					9																	35399243		2203	4300	6503	SO:0001583	missense	10497	exon33			ACAATGGAGAGGA	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3913G>A	9.37:g.35399243G>A	ENSP00000367756:p.Glu1305Lys	223.0	0.0	0		186.0	8.0	0.0430108	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688200	0.96784	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.75704	-0.96;-0.96;-0.96	6.08	6.08	0.98989	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.89136	0.6629	M	0.89095	3.005	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.995;0.998	D	0.89952	0.4080	10	0.87932	D	0	-22.8301	19.4349	0.94788	0.0:0.0:1.0:0.0	.	1305;1305	F8W8M9;O14795	.;UN13B_HUMAN	K	1317;1305;1305;892	ENSP00000380006:E1317K;ENSP00000367756:E1305K;ENSP00000367757:E1305K	ENSP00000367756:E1305K	E	+	1	0	UNC13B	35389243	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.338000	0.96553	2.894000	0.99253	0.655000	0.94253	GAG	.	.	none		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
TXN2	25828	hgsc.bcm.edu	37	22	36872873	36872873	+	Silent	SNP	C	C	T	rs150502647	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36872873C>T	ENST00000216185.2	-	3	760	c.294G>A	c.(292-294)ccG>ccA	p.P98P	TXN2_ENST00000416967.1_5'UTR|TXN2_ENST00000487725.1_5'UTR|TXN2_ENST00000403313.1_Silent_p.P98P			Q99757	THIOM_HUMAN	thioredoxin 2	98	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						TCTCTAACCTCGGCCCCAGGA	0.547													c|||	24	0.00479233	0.0	0.0144	5008	,	,		17737	0.0		0.0099	False		,,,				2504	0.0041				p.P98P		Atlas-SNP	.											.	TXN2	15	.	0			c.G294A						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	191.0	152.0	165.0		294	-10.3	0.0	22	dbSNP_134	165	81,8519	46.7+/-105.8	2,77,4221	no	coding-synonymous	TXN2	NM_012473.3		2,83,6418	TT,TC,CC		0.9419,0.1362,0.6689		98/167	36872873	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	25828	exon3			TAACCTCGGCCCC	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.294G>A	22.37:g.36872873C>T		120.0	0.0	0		138.0	67.0	0.485507	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Silent	SNP	ENST00000216185.2	37	CCDS13928.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473	
OR10G9	219870	hgsc.bcm.edu	37	11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123893757C>T	ENST00000375024.1	+	1	38	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TTCATCCTCACGGGCCTTCCC	0.562																																					p.T13M		Atlas-SNP	.											OR10G9,NS,carcinoma,0,2	OR10G9	80	2	0			c.C38T						scavenged	.						175.0	170.0	172.0					11																	123893757		2201	4299	6500	SO:0001583	missense	219870	exon1			TCCTCACGGGCCT	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.38C>T	11.37:g.123893757C>T	ENSP00000364164:p.Thr13Met	199.0	0.0	0		239.0	25.0	0.104603	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608309	0.14002	.	.	ENSG00000236981	ENST00000375024	T	0.00421	7.46	3.33	-4.34	0.03666	.	1.118960	0.06817	N	0.791372	T	0.00178	0.0005	N	0.04260	-0.245	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.29640	-1.0005	10	0.40728	T	0.16	.	9.7201	0.40297	0.0:0.2623:0.0:0.7377	.	13	Q8NGN4	O10G9_HUMAN	M	13	ENSP00000364164:T13M	ENSP00000364164:T13M	T	+	2	0	OR10G9	123398967	0.000000	0.05858	0.149000	0.22428	0.069000	0.16628	-0.761000	0.04751	-1.009000	0.03400	-0.766000	0.03442	ACG	.	.	none		0.562	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244199	11244199	+	Missense_Mutation	SNP	C	C	G	rs201245949	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11244199C>G	ENST00000531678.1	-	1	713	c.630G>C	c.(628-630)caG>caC	p.Q210H	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	210					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TACCATGGAGCTGCATCTTCT	0.408																																					p.Q210H		Atlas-SNP	.											.	TAS2R43	19	.	0			c.G630C						PASS	.						121.0	97.0	105.0					12																	11244199		2149	4144	6293	SO:0001583	missense	259289	exon1			ATGGAGCTGCATC	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.630G>C	12.37:g.11244199C>G	ENSP00000431719:p.Gln210His	26.0	0.0	0		103.0	12.0	0.116505	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	.	.	.	.	.	.	.	.	.	.	-	3.385	-0.125533	0.06795	.	.	ENSG00000255374	ENST00000531678	T	0.00966	5.49	1.45	-0.562	0.11781	.	.	.	.	.	T	0.01976	0.0062	M	0.83852	2.665	0.09310	N	1	B	0.18968	0.032	B	0.32724	0.151	T	0.38672	-0.9650	9	0.54805	T	0.06	.	3.9123	0.09209	0.0:0.53:0.0:0.47	.	210	P59537	T2R43_HUMAN	H	210	ENSP00000431719:Q210H	ENSP00000431719:Q210H	Q	-	3	2	TAS2R43	11135466	0.000000	0.05858	0.088000	0.20740	0.014000	0.08584	-0.691000	0.05133	-0.203000	0.10251	0.195000	0.17529	CAG	C|0.994;G|0.006	0.006	strong		0.408	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
KIF13B	23303	hgsc.bcm.edu	37	8	29033628	29033628	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:29033628T>G	ENST00000524189.1	-	10	940	c.902A>C	c.(901-903)aAa>aCa	p.K301T	KIF13B_ENST00000521515.1_Missense_Mutation_p.K301T	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	301	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		TGGAACAAATTTATTCTTGTT	0.423																																					p.K301T		Atlas-SNP	.											KIF13B_ENST00000524189,colon,carcinoma,+1,2	KIF13B	192	2	0			c.A902C						scavenged	.						79.0	74.0	76.0					8																	29033628		1895	4111	6006	SO:0001583	missense	23303	exon10			ACAAATTTATTCT	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.902A>C	8.37:g.29033628T>G	ENSP00000427900:p.Lys301Thr	81.0	0.0	0		61.0	3.0	0.0491803	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.642317	0.87859	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	T;T	0.75589	-0.95;-0.95	5.31	5.31	0.75309	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	T	0.79924	0.4530	L	0.37507	1.11	0.80722	D	1	D;D;B	0.89917	0.999;1.0;0.33	D;D;B	0.85130	0.997;0.994;0.257	T	0.77613	-0.2522	10	0.30078	T	0.28	.	15.4324	0.75112	0.0:0.0:0.0:1.0	.	287;301;301	C9JK41;Q9NQT8;F8VPJ2	.;KI13B_HUMAN;.	T	301	ENSP00000427900:K301T;ENSP00000429201:K301T	ENSP00000429201:K301T	K	-	2	0	KIF13B	29089547	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.803000	0.85983	2.231000	0.72958	0.460000	0.39030	AAA	.	.	none		0.423	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
DIS3	22894	hgsc.bcm.edu	37	13	73340177	73340177	+	Missense_Mutation	SNP	G	G	A	rs35017269	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:73340177G>A	ENST00000377767.4	-	15	2003	c.1903C>T	c.(1903-1905)Cct>Tct	p.P635S	DIS3_ENST00000545453.1_Missense_Mutation_p.P473S|DIS3_ENST00000377780.4_Missense_Mutation_p.P605S	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	635				P -> S (in Ref. 7; CAH56266). {ECO:0000305}.	CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		CGAACTTCAGGAGAGGATAGA	0.328										Multiple Myeloma(4;0.011)			G|||	41	0.0081869	0.003	0.0144	5008	,	,		13716	0.002		0.007	False		,,,				2504	0.0184				p.P635S		Atlas-SNP	.											.	DIS3	103	.	0			c.C1903T						PASS	.	G	SER/PRO,SER/PRO	14,4392	23.3+/-48.9	0,14,2189	43.0	42.0	43.0		1813,1903	6.0	1.0	13	dbSNP_126	43	134,8466	64.9+/-127.2	1,132,4167	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	74,74	1,146,6356	AA,AG,GG		1.5581,0.3177,1.1379	benign,benign	605/929,635/959	73340177	148,12858	2203	4300	6503	SO:0001583	missense	22894	exon15			CTTCAGGAGAGGA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1903C>T	13.37:g.73340177G>A	ENSP00000366997:p.Pro635Ser	23.0	0.0	0		25.0	15.0	0.6	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	18	0.008241758241758242	4	0.008130081300813009	8	0.022099447513812154	0	0.0	6	0.0079155672823219	G	16.70	3.197149	0.58126	0.003177	0.015581	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.38240	1.15;1.15;1.15	6.04	6.04	0.98038	Ribonuclease II/R (2);	0.054605	0.64402	D	0.000001	T	0.28267	0.0698	L	0.41356	1.27	0.58432	D	0.999999	P;P	0.41947	0.723;0.766	P;P	0.49387	0.474;0.609	T	0.00885	-1.1527	10	0.26408	T	0.33	.	20.5948	0.99439	0.0:0.0:1.0:0.0	rs35017269	605;635	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	S	635;605;473	ENSP00000366997:P635S;ENSP00000367011:P605S;ENSP00000440058:P473S	ENSP00000366997:P635S	P	-	1	0	DIS3	72238178	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.518000	0.73764	2.873000	0.98535	0.563000	0.77884	CCT	G|0.989;A|0.011	0.011	strong		0.328	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95696540C>T	ENST00000376887.4	-	28	3723	c.3609G>A	c.(3607-3609)gcG>gcA	p.A1203A	ABCC4_ENST00000412704.1_Silent_p.A1156A	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1203	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CATTTGCCGTCGCTTCATCAA	0.398													C|||	225	0.0449281	0.1604	0.013	5008	,	,		19815	0.001		0.002	False		,,,				2504	0.001				p.A1203A		Atlas-SNP	.											ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	0			c.G3609A						PASS	.	C		644,3762	270.4+/-269.6	52,540,1611	72.0	64.0	66.0		3609	-6.7	0.9	13	dbSNP_126	66	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ABCC4	NM_005845.3		52,550,5901	TT,TC,CC		0.1163,14.6164,5.0284		1203/1326	95696540	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon28			TGCCGTCGCTTCA	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3609G>A	13.37:g.95696540C>T		95.0	0.0	0		126.0	72.0	0.571429	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			C|0.950;T|0.050	0.050	strong		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
SUV39H1	6839	hgsc.bcm.edu	37	X	48558888	48558888	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48558888C>T	ENST00000376687.3	+	3	762	c.572C>T	c.(571-573)aCt>aTt	p.T191I	SUV39H1_ENST00000453214.2_Intron|SUV39H1_ENST00000337852.6_Missense_Mutation_p.T202I|AF196970.3_ENST00000416061.1_RNA	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	191	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|chromatin silencing at rDNA (GO:0000183)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin silencing complex (GO:0005677)|chromosome, centromeric region (GO:0000775)|condensed nuclear chromosome (GO:0000794)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|rDNA heterochromatin (GO:0033553)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|protein N-terminus binding (GO:0047485)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						TGGGCACCCACTGGAGGCTGC	0.632																																					p.T191I		Atlas-SNP	.											.	SUV39H1	36	.	0			c.C572T						PASS	.						52.0	41.0	45.0					X																	48558888		2203	4300	6503	SO:0001583	missense	6839	exon3			CACCCACTGGAGG	AF019968	CCDS14304.1, CCDS65252.1	Xp11.23	2011-07-01	2001-11-28		ENSG00000101945	ENSG00000101945		"""Chromatin-modifying enzymes / K-methyltransferases"""	11479	protein-coding gene	gene with protein product		300254	"""suppressor of variegation 3-9 (Drosophila) homolog 1"""	SUV39H		10202156	Standard	NM_001282166		Approved	KMT1A	uc004dkn.3	O43463	OTTHUMG00000022701	ENST00000376687.3:c.572C>T	X.37:g.48558888C>T	ENSP00000365877:p.Thr191Ile	86.0	0.0	0		94.0	52.0	0.553191	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Missense_Mutation	SNP	ENST00000376687.3	37	CCDS14304.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237725	0.39598	.	.	ENSG00000101945	ENST00000337852;ENST00000376687;ENST00000448548;ENST00000422496	D;D	0.89270	-2.49;-2.49	4.93	3.13	0.36017	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	0.478513	0.21039	N	0.081202	T	0.77246	0.4102	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.11235	0.004;0.002	B;B	0.15870	0.014;0.014	T	0.63278	-0.6673	10	0.36615	T	0.2	.	4.2419	0.10652	0.1806:0.6131:0.0:0.2062	.	202;191	B4DST0;O43463	.;SUV91_HUMAN	I	202;191;189;49	ENSP00000337976:T202I;ENSP00000365877:T191I	ENSP00000337976:T202I	T	+	2	0	SUV39H1	48443832	0.019000	0.18553	0.882000	0.34594	0.989000	0.77384	1.055000	0.30467	0.858000	0.35431	0.502000	0.49764	ACT	.	.	none		0.632	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173	
CSDE1	7812	hgsc.bcm.edu	37	1	115272916	115272916	+	Missense_Mutation	SNP	T	T	C	rs149300730		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:115272916T>C	ENST00000358528.4	-	12	1745	c.1319A>G	c.(1318-1320)aAt>aGt	p.N440S	CSDE1_ENST00000530886.1_Missense_Mutation_p.N310S|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Missense_Mutation_p.N455S|CSDE1_ENST00000261443.5_Missense_Mutation_p.N409S|CSDE1_ENST00000438362.2_Missense_Mutation_p.N486S|CSDE1_ENST00000339438.6_Missense_Mutation_p.N409S|CSDE1_ENST00000534699.1_Missense_Mutation_p.N440S	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	440					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGTTTTAGGATTGGAAAAAGT	0.388																																					p.N486S		Atlas-SNP	.											.	CSDE1	145	.	0			c.A1457G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	130.0	137.0	135.0		1319,1364,1457,1319,1226,1226	4.5	1.0	1	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense	CSDE1	NM_001007553.2,NM_001130523.2,NM_001242891.1,NM_001242892.1,NM_001242893.1,NM_007158.5	46,46,46,46,46,46	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	440/799,455/814,486/845,440/799,409/768,409/768	115272916	2,13004	2203	4300	6503	SO:0001583	missense	7812	exon13			TTAGGATTGGAAA		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1319A>G	1.37:g.115272916T>C	ENSP00000351329:p.Asn440Ser	100.0	0.0	0		108.0	39.0	0.361111	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.843379	0.32606	0.0	2.33E-4	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	5.61	4.48	0.54585	.	0.393339	0.26072	N	0.026508	T	0.41119	0.1145	L	0.36672	1.1	0.35973	D	0.835437	B;B;D	0.56035	0.243;0.007;0.974	B;B;D	0.67725	0.079;0.011;0.953	T	0.36504	-0.9745	9	0.09084	T	0.74	-10.7066	11.1387	0.48390	0.0:0.0:0.1548:0.8452	.	455;440;486	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	S	409;486;440;409;310;455;440	.	ENSP00000261443:N409S	N	-	2	0	CSDE1	115074439	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	2.729000	0.47327	0.949000	0.37715	-0.313000	0.08912	AAT	T|1.000;C|0.000	0.000	weak		0.388	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
NAA15	80155	hgsc.bcm.edu	37	4	140264020	140264020	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:140264020G>A	ENST00000296543.5	+	5	766	c.443G>A	c.(442-444)aGa>aAa	p.R148K	NAA15_ENST00000398947.1_Missense_Mutation_p.R148K|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	148					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CCTGCGCAGAGAGCATCATGG	0.348																																					p.R148K		Atlas-SNP	.											.	NAA15	88	.	0			c.G443A						PASS	.						137.0	127.0	130.0					4																	140264020		1857	4118	5975	SO:0001583	missense	80155	exon5			CGCAGAGAGCATC	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.443G>A	4.37:g.140264020G>A	ENSP00000296543:p.Arg148Lys	137.0	0.0	0		128.0	40.0	0.3125	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334046	0.81801	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.52526	0.66;0.66	5.25	5.25	0.73442	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.066107	0.64402	D	0.000018	T	0.53061	0.1773	M	0.76170	2.325	0.80722	D	1	P	0.38922	0.651	B	0.38194	0.267	T	0.55945	-0.8060	10	0.41790	T	0.15	-13.5405	19.4069	0.94651	0.0:0.0:1.0:0.0	.	148	Q9BXJ9	NAA15_HUMAN	K	148;22;148	ENSP00000296543:R148K;ENSP00000381920:R148K	ENSP00000296543:R148K	R	+	2	0	NAA15	140483470	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.075000	0.94004	2.894000	0.99253	0.591000	0.81541	AGA	.	.	none		0.348	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
PSG11	5680	hgsc.bcm.edu	37	19	43519324	43519324	+	Missense_Mutation	SNP	G	G	A	rs139355393		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43519324G>A	ENST00000401740.1	-	4	1011	c.908C>T	c.(907-909)gCt>gTt	p.A303V	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000320078.7_Missense_Mutation_p.A303V|PSG11_ENST00000306322.7_Missense_Mutation_p.A181V|PSG11_ENST00000403486.1_Missense_Mutation_p.A181V			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	312	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				TGAGTTACGAGCAGAGCAAGC	0.458													.|||	1	0.000199681	0.0	0.0	5008	,	,		20595	0.001		0.0	False		,,,				2504	0.0				p.A303V		Atlas-SNP	.											.	PSG11	57	.	0			c.C908T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	2,4396	4.2+/-10.8	1,0,2198	147.0	142.0	144.0		542,908,542	-2.0	0.0	19	dbSNP_134	144	6,8588	5.0+/-18.6	0,6,4291	yes	missense,missense,missense	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	64,64,64	1,6,6489	AA,AG,GG		0.0698,0.0455,0.0616	,,	181/214,303/336,181/214	43519324	8,12984	2199	4297	6496	SO:0001583	missense	5680	exon4			TTACGAGCAGAGC	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.908C>T	19.37:g.43519324G>A	ENSP00000384995:p.Ala303Val	120.0	0.0	0		102.0	49.0	0.480392	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	g	0	-2.632599	0.00115	4.55E-4	6.98E-4	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	0.976	-1.95	0.07548	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56645	0.1999	L	0.31926	0.97	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.45716	-0.9242	9	0.02654	T	1	.	4.5197	0.11954	0.5126:0.0:0.4874:0.0	.	181;303	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	V	303;181;181;303	ENSP00000319140:A303V;ENSP00000385427:A181V;ENSP00000304913:A181V;ENSP00000384995:A303V	ENSP00000304913:A181V	A	-	2	0	PSG11	48211164	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-1.321000	0.02697	-1.482000	0.01860	-1.207000	0.01640	GCT	G|1.000;A|0.000	0.000	weak		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
UHRF2	115426	hgsc.bcm.edu	37	9	6413515	6413515	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413515G>C	ENST00000276893.5	+	1	193	c.25G>C	c.(25-27)Gat>Cat	p.D9H	UHRF2_ENST00000381373.3_Missense_Mutation_p.D9H|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	9	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		TCGCACCATTGATGGCTCCAA	0.662																																					p.D9H		Atlas-SNP	.											UHRF2,NS,carcinoma,-1,1	UHRF2	50	1	0			c.G25C						PASS	.						60.0	60.0	60.0					9																	6413515		2203	4300	6503	SO:0001583	missense	115426	exon1			ACCATTGATGGCT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.25G>C	9.37:g.6413515G>C	ENSP00000276893:p.Asp9His	87.0	0.0	0		77.0	14.0	0.181818	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	G	33	5.248236	0.95305	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.12361	2.69;2.69	4.87	4.87	0.63330	Ubiquitin supergroup (1);Ubiquitin (2);	0.056041	0.64402	D	0.000002	T	0.45836	0.1362	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55786	-0.8086	10	0.87932	D	0	-12.9077	17.7967	0.88574	0.0:0.0:1.0:0.0	.	9	Q96PU4	UHRF2_HUMAN	H	9	ENSP00000276893:D9H;ENSP00000370778:D9H	ENSP00000276893:D9H	D	+	1	0	UHRF2	6403515	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.728000	0.91484	2.526000	0.85167	0.561000	0.74099	GAT	.	.	none		0.662	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
FAM83H	286077	hgsc.bcm.edu	37	8	144808953	144808953	+	Missense_Mutation	SNP	G	G	T	rs200179667	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144808953G>T	ENST00000388913.3	-	5	2803	c.2678C>A	c.(2677-2679)cCa>cAa	p.P893Q		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	893					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TCCTGTAGTTGGACTTCCTCT	0.637													g|||	11	0.00219649	0.0083	0.0	5008	,	,		13854	0.0		0.0	False		,,,				2504	0.0				p.P893Q		Atlas-SNP	.											.	FAM83H	68	.	0			c.C2678A						PASS	.		GLN/PRO	11,3803		0,11,1896	22.0	23.0	23.0		2678	4.4	0.5	8		23	4,8216		0,4,4106	yes	missense	FAM83H	NM_198488.3	76	0,15,6002	TT,TG,GG		0.0487,0.2884,0.1246	probably-damaging	893/1180	144808953	15,12019	1907	4110	6017	SO:0001583	missense	286077	exon5			GTAGTTGGACTTC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2678C>A	8.37:g.144808953G>T	ENSP00000373565:p.Pro893Gln	62.0	0.0	0		47.0	22.0	0.468085	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	5.326	0.245407	0.10077	0.002884	4.87E-4	ENSG00000180921	ENST00000388913	T	0.51574	0.7	4.4	4.4	0.53042	.	1.318910	0.05373	N	0.535775	T	0.33177	0.0854	N	0.17082	0.46	0.09310	N	1	B	0.30584	0.286	B	0.25884	0.064	T	0.12319	-1.0552	10	0.34782	T	0.22	.	9.1646	0.37043	0.0:0.1571:0.681:0.1619	.	893	Q6ZRV2	FA83H_HUMAN	Q	893	ENSP00000373565:P893Q	ENSP00000373565:P893Q	P	-	2	0	FAM83H	144880941	1.000000	0.71417	0.511000	0.27724	0.126000	0.20510	3.435000	0.52849	2.165000	0.68154	0.556000	0.70494	CCA	G|0.999;T|0.001	0.001	strong		0.637	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
ART5	116969	hgsc.bcm.edu	37	11	3660238	3660238	+	Missense_Mutation	SNP	G	G	A	rs142998376	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3660238G>A	ENST00000397068.3	-	3	1207	c.815C>T	c.(814-816)gCg>gTg	p.A272V	TRPC2_ENST00000526541.1_RNA|ART5_ENST00000397067.3_Missense_Mutation_p.A204V|ART5_ENST00000359918.4_Missense_Mutation_p.A272V	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	272					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCACCTGGCGCAGACACACA	0.637													G|||	17	0.00339457	0.0091	0.0072	5008	,	,		16924	0.0		0.0	False		,,,				2504	0.0				p.A272V		Atlas-SNP	.											.	ART5	38	.	0			c.C815T						PASS	.	G	VAL/ALA,VAL/ALA	18,4314		0,18,2148	60.0	52.0	55.0		815,815	-8.6	0.0	11	dbSNP_134	55	16,8478		0,16,4231	yes	missense,missense	ART5	NM_001079536.1,NM_053017.3	64,64	0,34,6379	AA,AG,GG		0.1884,0.4155,0.2651	benign,benign	272/292,272/292	3660238	34,12792	2166	4247	6413	SO:0001583	missense	116969	exon3			CCTGGCGCAGACA	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.815C>T	11.37:g.3660238G>A	ENSP00000380258:p.Ala272Val	83.0	0.0	0		73.0	33.0	0.452055	NM_053017	C9IYG7|Q6UX84|Q86W02	Missense_Mutation	SNP	ENST00000397068.3	37	CCDS7743.1	5	0.0022893772893772895	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	0	0.0	G	8.738	0.918215	0.17982	0.004155	0.001884	ENSG00000167311	ENST00000397068;ENST00000397067;ENST00000359918	T;T;T	0.08458	3.09;3.17;3.09	5.87	-8.63	0.00878	.	3.067170	0.00805	N	0.001445	T	0.02494	0.0076	N	0.11927	0.2	0.09310	N	1	B;B	0.25206	0.12;0.0	B;B	0.21917	0.037;0.0	T	0.32428	-0.9907	10	0.27785	T	0.31	7.2848	4.0976	0.09998	0.1934:0.1975:0.5108:0.0983	.	204;272	Q96L15-2;Q96L15	.;NAR5_HUMAN	V	272;204;272	ENSP00000380258:A272V;ENSP00000380257:A204V;ENSP00000352992:A272V	ENSP00000352992:A272V	A	-	2	0	ART5	3616814	0.000000	0.05858	0.000000	0.03702	0.542000	0.35054	-1.166000	0.03129	-1.233000	0.02551	0.655000	0.94253	GCG	G|0.998;A|0.002	0.002	strong		0.637	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017	
DHX34	9704	hgsc.bcm.edu	37	19	47858526	47858526	+	Silent	SNP	C	C	T	rs138629177		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47858526C>T	ENST00000328771.4	+	3	1285	c.936C>T	c.(934-936)gcC>gcT	p.A312A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	312	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TCATGTCGGCCACCATCAACA	0.587																																					p.A312A		Atlas-SNP	.											.	DHX34	98	.	0			c.C936T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	162.0	144.0	150.0		936	2.2	1.0	19	dbSNP_134	150	0,8600		0,0,4300	no	coding-synonymous	DHX34	NM_014681.5		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		312/1144	47858526	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9704	exon3			GTCGGCCACCATC	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.936C>T	19.37:g.47858526C>T		122.0	0.0	0		105.0	53.0	0.504762	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			C|1.000;T|0.000	0.000	weak		0.587	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
BCL9	607	hgsc.bcm.edu	37	1	147090956	147090956	+	Missense_Mutation	SNP	C	C	T	rs61751616	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:147090956C>T	ENST00000234739.3	+	8	1735	c.995C>T	c.(994-996)cCg>cTg	p.P332L		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	332	Poly-Pro.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					AAAGCCCCTCCGCCTCCACCA	0.612			T	"""IGH@, IGL@"""	B-ALL								C|||	25	0.00499201	0.0008	0.0043	5008	,	,		15292	0.0		0.0209	False		,,,				2504	0.0				p.P332L		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.C995T						PASS	.	C	LEU/PRO	12,4394	19.1+/-41.9	0,12,2191	58.0	64.0	62.0		995	4.6	0.9	1	dbSNP_129	62	119,8481	61.3+/-123.2	1,117,4182	yes	missense	BCL9	NM_004326.2	98	1,129,6373	TT,TC,CC		1.3837,0.2724,1.0072	benign	332/1427	147090956	131,12875	2203	4300	6503	SO:0001583	missense	607	exon8			CCCCTCCGCCTCC	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.995C>T	1.37:g.147090956C>T	ENSP00000234739:p.Pro332Leu	25.0	0.0	0		46.0	23.0	0.5	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	20	0.009157509157509158	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	17	0.022427440633245383	C	7.697	0.692207	0.15039	0.002724	0.013837	ENSG00000116128	ENST00000234739	T	0.55052	0.54	5.61	4.63	0.57726	.	0.293568	0.38326	N	0.001739	T	0.17746	0.0426	N	0.12182	0.205	0.35771	D	0.820903	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03717	-1.1010	10	0.25106	T	0.35	-4.5305	11.3271	0.49454	0.0:0.907:0.0:0.093	rs61751616	332;332	Q1JQ81;O00512	.;BCL9_HUMAN	L	332	ENSP00000234739:P332L	ENSP00000234739:P332L	P	+	2	0	BCL9	145557580	0.702000	0.27816	0.858000	0.33744	0.685000	0.39939	2.819000	0.48049	2.937000	0.99478	0.650000	0.86243	CCG	C|0.990;T|0.010	0.010	strong		0.612	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709723	31709723	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31709723A>C	ENST00000382835.2	-	1	289	c.264T>G	c.(262-264)acT>acG	p.T88T		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	88						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						AATTGGAGTAAGTAGTTTGGA	0.488																																					p.T88T		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.T264G						PASS	.						149.0	145.0	146.0					21																	31709723		2203	4300	6503	SO:0001819	synonymous_variant	643812	exon1			GGAGTAAGTAGTT	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.264T>G	21.37:g.31709723A>C		157.0	0.0	0		230.0	45.0	0.195652	NM_001077711		Silent	SNP	ENST00000382835.2	37	CCDS33532.1																																																																																			.	.	none		0.488	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
SPIDR	23514	hgsc.bcm.edu	37	8	48612997	48612997	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:48612997T>A	ENST00000297423.4	+	12	2102	c.1718T>A	c.(1717-1719)cTg>cAg	p.L573Q	SPIDR_ENST00000517693.1_Missense_Mutation_p.L48Q|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.L503Q|SPIDR_ENST00000518074.1_Missense_Mutation_p.L513Q	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	573					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											ATTGACACCCTGTGGCCCCCA	0.522																																					p.L573Q		Atlas-SNP	.											.	KIAA0146	64	.	0			c.T1718A						PASS	.						185.0	178.0	180.0					8																	48612997		1913	4115	6028	SO:0001583	missense	23514	exon12			ACACCCTGTGGCC	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1718T>A	8.37:g.48612997T>A	ENSP00000297423:p.Leu573Gln	119.0	0.0	0		103.0	10.0	0.0970874	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.90|14.90	2.672941|2.672941	0.47781|0.47781	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000519401|ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362	.|.	.|.	.|.	5.41|5.41	4.25|4.25	0.50352|0.50352	.|.	.|0.646742	.|0.16164	.|N	.|0.226637	T|T	0.60907|0.60907	0.2305|0.2305	L|L	0.58101|0.58101	1.795|1.795	0.30107|0.30107	N|N	0.806873|0.806873	.|D;D;D;P;D;P;D;P	.|0.67145	.|0.989;0.989;0.996;0.95;0.989;0.95;0.996;0.95	.|D;D;D;P;D;P;D;P	.|0.66351	.|0.912;0.912;0.931;0.776;0.912;0.776;0.943;0.776	T|T	0.60316|0.60316	-0.7287|-0.7287	5|9	.|0.87932	.|D	.|0	.|.	9.5224|9.5224	0.39143|0.39143	0.0:0.0811:0.0:0.9189|0.0:0.0811:0.0:0.9189	.|.	.|63;78;513;503;573;262;48;573	.|B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B4DEV5;B4DFT3;B3KP42;Q14159	.|.;.;.;.;.;.;.;K0146_HUMAN	S|Q	255|573;513;503;78;48;48	.|.	.|ENSP00000297423:L573Q	C|L	+|+	1|2	0|0	KIAA0146|KIAA0146	48775550|48775550	0.964000|0.964000	0.33143|0.33143	0.065000|0.065000	0.19835|0.19835	0.150000|0.150000	0.21749|0.21749	2.139000|2.139000	0.42149|0.42149	0.889000|0.889000	0.36185|0.36185	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	none		0.522	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394	
DNHD1	144132	hgsc.bcm.edu	37	11	6578788	6578788	+	Missense_Mutation	SNP	C	C	T	rs111982303	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6578788C>T	ENST00000527990.2	+	23	8263	c.8263C>T	c.(8263-8265)Cca>Tca	p.P2755S	DNHD1_ENST00000254579.6_Missense_Mutation_p.P2755S			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2755					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ATCCATAGGACCAGTAAGCAG	0.473													C|||	114	0.0227636	0.0061	0.0245	5008	,	,		22472	0.0099		0.004	False		,,,				2504	0.0767				p.P2755S		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8263T						PASS	.	C	SER/PRO	10,1374		0,10,682	81.0	81.0	81.0		8263	0.2	0.0	11	dbSNP_132	81	25,3157		0,25,1566	yes	missense	DNHD1	NM_144666.2	74	0,35,2248	TT,TC,CC		0.7857,0.7225,0.7665	benign	2755/4754	6578788	35,4531	692	1591	2283	SO:0001583	missense	144132	exon25			ATAGGACCAGTAA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8263C>T	11.37:g.6578788C>T	ENSP00000436180:p.Pro2755Ser	71.0	0.0	0		62.0	38.0	0.612903	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	26	0.011904761904761904	4	0.008130081300813009	9	0.024861878453038673	10	0.017482517482517484	3	0.00395778364116095	C	0.280	-0.986911	0.02180	0.007225	0.007857	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.25912	1.77;1.77	4.91	0.165	0.14995	.	.	.	.	.	T	0.04272	0.0118	N	0.08118	0	0.09310	N	1	B;B	0.22909	0.01;0.077	B;B	0.20767	0.007;0.031	T	0.34601	-0.9822	9	0.14252	T	0.57	.	2.3474	0.04275	0.1445:0.5153:0.1405:0.1997	.	2755;502	Q96M86;E9PHZ7	DNHD1_HUMAN;.	S	2755;2755;502	ENSP00000254579:P2755S;ENSP00000436180:P2755S	ENSP00000254579:P2755S	P	+	1	0	DNHD1	6535364	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.244000	0.08903	-0.116000	0.11893	-0.266000	0.10368	CCA	C|0.988;T|0.012	0.012	strong		0.473	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
C17orf70	80233	hgsc.bcm.edu	37	17	79517729	79517729	+	Missense_Mutation	SNP	G	G	A	rs62076033	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79517729G>A	ENST00000327787.8	-	3	837	c.791C>T	c.(790-792)gCc>gTc	p.A264V	C17orf70_ENST00000537152.1_Missense_Mutation_p.A113V|C17orf70_ENST00000425898.2_5'Flank			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	264					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GTCACCAGGGGCTGACCTGGA	0.597													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17976	0.001		0.005	False		,,,				2504	0.0051				p.A264V		Atlas-SNP	.											.	C17orf70	79	.	0			c.C791T						PASS	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	50.0	49.0	49.0		791	1.3	0.0	17	dbSNP_129	49	35,8565	24.0+/-70.4	1,33,4266	yes	missense	C17orf70	NM_025161.5	64	1,35,6467	AA,AG,GG		0.407,0.0454,0.2845	possibly-damaging	264/882	79517729	37,12969	2203	4300	6503	SO:0001583	missense	80233	exon3			CCAGGGGCTGACC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.791C>T	17.37:g.79517729G>A	ENSP00000333283:p.Ala264Val	83.0	0.0	0		79.0	36.0	0.455696	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	37	CCDS32765.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	14.74	2.625913	0.46840	4.54E-4	0.00407	ENSG00000185504	ENST00000327787;ENST00000537152;ENST00000541246;ENST00000544302	T;T	0.34472	1.36;1.36	4.34	1.27	0.21489	.	0.691562	0.13293	N	0.398824	T	0.24547	0.0595	L	0.51422	1.61	0.09310	N	1	P	0.40731	0.728	P	0.46076	0.503	T	0.16837	-1.0389	10	0.42905	T	0.14	.	0.873	0.01218	0.2856:0.159:0.3926:0.1628	rs62076033	264	Q0VG06	FP100_HUMAN	V	264;113;113;113	ENSP00000333283:A264V;ENSP00000440151:A113V	ENSP00000333283:A264V	A	-	2	0	C17orf70	77128171	0.931000	0.31567	0.028000	0.17463	0.604000	0.37047	2.557000	0.45871	0.129000	0.18514	0.563000	0.77884	GCC	G|0.997;A|0.003	0.003	strong		0.597	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637053	111637053	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111637053T>C	ENST00000527614.1	-	1	98	c.33A>G	c.(31-33)ccA>ccG	p.P11P	PPP2R1B_ENST00000341980.6_Silent_p.P11P|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000426998.2_Silent_p.P11P|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000311129.5_Silent_p.P11P|PPP2R1B_ENST00000393055.2_Silent_p.P11P	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	11					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CCGCTGCTCCTGGGCCGGTCC	0.672																																					p.P11P		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A33G						PASS	.						60.0	59.0	59.0					11																	111637053		2201	4297	6498	SO:0001819	synonymous_variant	5519	exon1			TGCTCCTGGGCCG	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.33A>G	11.37:g.111637053T>C		25.0	0.0	0		35.0	17.0	0.485714	NM_001177562	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Silent	SNP	ENST00000527614.1	37	CCDS8349.1																																																																																			.	.	none		0.672	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
MYO9A	4649	hgsc.bcm.edu	37	15	72189925	72189925	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:72189925C>T	ENST00000356056.5	-	25	5391	c.4919G>A	c.(4918-4920)cGc>cAc	p.R1640H	MYO9A_ENST00000566885.1_Missense_Mutation_p.R1260H|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000444904.1_Missense_Mutation_p.R1621H|MYO9A_ENST00000564571.1_Missense_Mutation_p.R1640H|MYO9A_ENST00000424560.1_Missense_Mutation_p.R1640H	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1640	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTTGAAATGCGATTATTTGA	0.428																																					p.R1640H		Atlas-SNP	.											.	MYO9A	203	.	0			c.G4919A						PASS	.						156.0	139.0	145.0					15																	72189925		2199	4297	6496	SO:0001583	missense	4649	exon25			GAAATGCGATTAT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.4919G>A	15.37:g.72189925C>T	ENSP00000348349:p.Arg1640His	229.0	0.0	0		192.0	52.0	0.270833	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	c	5.821	0.335743	0.11013	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.84223	-1.82;-1.82;-1.81	5.19	1.26	0.21427	.	.	.	.	.	T	0.70613	0.3244	N	0.17082	0.46	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.0	T	0.58278	-0.7664	9	0.45353	T	0.12	.	4.8546	0.13554	0.0:0.3852:0.2157:0.3991	.	1621;1640;1640	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	H	1640;1640;1621	ENSP00000348349:R1640H;ENSP00000399162:R1640H;ENSP00000398250:R1621H	ENSP00000348349:R1640H	R	-	2	0	MYO9A	69976979	0.000000	0.05858	0.035000	0.18076	0.984000	0.73092	-0.449000	0.06812	0.424000	0.26061	-0.127000	0.14921	CGC	.	.	none		0.428	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
UTP20	27340	hgsc.bcm.edu	37	12	101779435	101779435	+	Silent	SNP	T	T	C	rs149160478		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101779435T>C	ENST00000261637.4	+	61	8305	c.8131T>C	c.(8131-8133)Tta>Cta	p.L2711L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2711					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GAGCTTCTCATTAGCCTTTGC	0.423																																					p.L2711L		Atlas-SNP	.											.	UTP20	222	.	0			c.T8131C						PASS	.			1,4405	2.1+/-5.4	0,1,2202	88.0	89.0	89.0		8131	-3.6	0.0	12	dbSNP_134	89	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	UTP20	NM_014503.2		0,3,6500	CC,CT,TT		0.0233,0.0227,0.0231		2711/2786	101779435	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon61			TTCTCATTAGCCT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.8131T>C	12.37:g.101779435T>C		97.0	0.0	0		95.0	49.0	0.515789	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			T|1.000;C|0.000	0.000	weak		0.423	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
TREML2	79865	hgsc.bcm.edu	37	6	41166063	41166063	+	Missense_Mutation	SNP	C	C	A	rs147506354	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41166063C>A	ENST00000483722.1	-	2	345	c.160G>T	c.(160-162)Gtt>Ttt	p.V54F		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	54	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TTGCACCAAACCTTGCCCTCC	0.547																																					p.V54F		Atlas-SNP	.											.	TREML2	41	.	0			c.G160T						PASS	.	C	PHE/VAL	0,4406		0,0,2203	171.0	179.0	176.0		160	3.8	1.0	6	dbSNP_134	176	14,8586		0,14,4286	yes	missense	TREML2	NM_024807.2	50	0,14,6489	AA,AC,CC		0.1628,0.0,0.1076	probably-damaging	54/322	41166063	14,12992	2203	4300	6503	SO:0001583	missense	79865	exon2			ACCAAACCTTGCC	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.160G>T	6.37:g.41166063C>A	ENSP00000418767:p.Val54Phe	75.0	0.0	0		72.0	59.0	0.819444	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	15.93	2.976798	0.53720	0.0	0.001628	ENSG00000112195	ENST00000483722	T	0.64991	-0.13	4.75	3.84	0.44239	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.430853	0.19331	N	0.116887	T	0.54367	0.1854	L	0.47716	1.5	0.27559	N	0.950258	D	0.76494	0.999	D	0.75020	0.985	T	0.45977	-0.9224	10	0.17832	T	0.49	-4.2985	10.1612	0.42853	0.2078:0.7922:0.0:0.0	.	54	Q5T2D2	TRML2_HUMAN	F	54	ENSP00000418767:V54F	ENSP00000418767:V54F	V	-	1	0	TREML2	41274041	0.996000	0.38824	0.968000	0.41197	0.601000	0.36947	0.775000	0.26689	1.054000	0.40438	0.563000	0.77884	GTT	C|0.998;A|0.002	0.002	strong		0.547	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
SGK1	6446	hgsc.bcm.edu	37	6	134495674	134495674	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495674C>T	ENST00000237305.7	-	2	215	c.127G>A	c.(127-129)Gcc>Acc	p.A43T	SGK1_ENST00000528577.1_Missense_Mutation_p.A71T|SGK1_ENST00000413996.3_Missense_Mutation_p.A57T|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.A33T|SGK1_ENST00000475719.2_Missense_Mutation_p.A43T|SGK1_ENST00000367858.5_Missense_Mutation_p.A138T	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	43	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GAGTTATTGGCAATCTTCTGA	0.413											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A138T		Atlas-SNP	.											.	SGK1	387	.	0			c.G412A						PASS	.						91.0	89.0	90.0					6																	134495674		2203	4300	6503	SO:0001583	missense	6446	exon4			TATTGGCAATCTT	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.127G>A	6.37:g.134495674C>T	ENSP00000237305:p.Ala43Thr	71.0	0.0	0	1611	45.0	7.0	0.155556	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296537	0.81025	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.42900	1.51;1.51;1.51;1.51;1.51;1.51;0.96	5.89	5.89	0.94794	.	0.047350	0.85682	D	0.000000	T	0.33177	0.0854	L	0.51422	1.61	0.80722	D	1	B;B;B;B;B;B	0.29988	0.217;0.264;0.046;0.077;0.217;0.046	B;B;B;B;B;B	0.31946	0.098;0.124;0.045;0.098;0.138;0.028	T	0.17349	-1.0372	10	0.62326	D	0.03	.	20.2576	0.98430	0.0:1.0:0.0:0.0	.	71;57;43;33;138;43	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	T	138;57;43;33;71;43;107	ENSP00000356832:A138T;ENSP00000396242:A57T;ENSP00000237305:A43T;ENSP00000356831:A33T;ENSP00000434450:A71T;ENSP00000434302:A43T;ENSP00000435577:A107T	ENSP00000237305:A43T	A	-	1	0	SGK1	134537367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.766000	0.62279	2.783000	0.95769	0.655000	0.94253	GCC	.	.	none		0.413	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
RXFP2	122042	hgsc.bcm.edu	37	13	32367033	32367033	+	Missense_Mutation	SNP	C	C	G	rs138951290		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32367033C>G	ENST00000298386.2	+	16	1665	c.1594C>G	c.(1594-1596)Cga>Gga	p.R532G	RXFP2_ENST00000380314.1_Missense_Mutation_p.R508G	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	532					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		CAGTAACATTCGACCTGGAAA	0.453													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18297	0.0		0.0	False		,,,				2504	0.0				p.R532G		Atlas-SNP	.											RXFP2,NS,carcinoma,0,1	RXFP2	95	1	0			c.C1594G						PASS	.	C	GLY/ARG,GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	100.0	90.0	93.0		1522,1594	5.7	0.6	13	dbSNP_134	93	9,8591	7.7+/-29.5	0,9,4291	yes	missense,missense	RXFP2	NM_001166058.1,NM_130806.3	125,125	0,10,6493	GG,GC,CC		0.1047,0.0227,0.0769	probably-damaging,probably-damaging	508/731,532/755	32367033	10,12996	2203	4300	6503	SO:0001583	missense	122042	exon16			AACATTCGACCTG	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"""GPCR / Class A : Relaxin family peptide receptors"""	17318	protein-coding gene	gene with protein product		606655	"""leucine-rich repeat-containing G protein-coupled receptor 8"""	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1594C>G	13.37:g.32367033C>G	ENSP00000298386:p.Arg532Gly	114.0	0.0	0		138.0	67.0	0.485507	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361723	0.61403	2.27E-4	0.001047	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.39592	1.07;1.07	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.051378	0.85682	D	0.000000	T	0.62612	0.2442	M	0.89534	3.04	0.58432	D	0.999996	B;B	0.26445	0.149;0.149	B;B	0.39185	0.293;0.168	T	0.65915	-0.6052	10	0.72032	D	0.01	.	18.4913	0.90849	0.0:1.0:0.0:0.0	.	508;532	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	G	508;532	ENSP00000369670:R508G;ENSP00000298386:R532G	ENSP00000298386:R532G	R	+	1	2	RXFP2	31265033	0.033000	0.19621	0.590000	0.28732	0.958000	0.62258	0.768000	0.26590	2.721000	0.93114	0.655000	0.94253	CGA	C|0.999;G|0.001	0.001	strong		0.453	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:203157538A>G	ENST00000264279.5	+	9	1045	c.819A>G	c.(817-819)gaA>gaG	p.E273E	SNORD11B_ENST00000607707.1_RNA|SNORD11_ENST00000459124.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	273					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.E273E(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGCTCTATGAATATCTACAAA	0.368													A|||	31	0.0061901	0.0	0.0187	5008	,	,		18977	0.0		0.0159	False		,,,				2504	0.002				p.E273E		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	1	Substitution - coding silent(1)	prostate(1)	c.A819G						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	159.0	160.0	160.0		819	0.3	1.0	2	dbSNP_123	160	133,8467	67.0+/-129.4	3,127,4170	no	coding-synonymous	NOP58	NM_015934.3		3,139,6361	GG,GA,AA		1.5465,0.2724,1.1149		273/530	203157538	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon9			CTATGAATATCTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.819A>G	2.37:g.203157538A>G		116.0	0.0	0		132.0	66.0	0.5	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
RABGGTB	5876	hgsc.bcm.edu	37	1	76260248	76260248	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:76260248A>C	ENST00000319942.3	+	9	980	c.909A>C	c.(907-909)gaA>gaC	p.E303D	RABGGTB_ENST00000496055.1_3'UTR|MSH4_ENST00000263187.3_5'Flank|RABGGTB_ENST00000535300.1_Missense_Mutation_p.E129D	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	303					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						TTTTGGGAGAAGAACAGATTA	0.353																																					p.E303D		Atlas-SNP	.											.	RABGGTB	37	.	0			c.A909C						PASS	.						111.0	114.0	113.0					1																	76260248		2203	4300	6503	SO:0001583	missense	5876	exon9			GGGAGAAGAACAG	U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.909A>C	1.37:g.76260248A>C	ENSP00000317473:p.Glu303Asp	72.0	0.0	0		78.0	20.0	0.25641	NM_004582	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272993	0.40194	.	.	ENSG00000137955	ENST00000535300;ENST00000319942	T;T	0.42900	0.96;0.96	5.55	1.78	0.24846	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.242531	0.47852	N	0.000216	T	0.09774	0.0240	N	0.20766	0.605	0.42372	D	0.992459	B	0.02656	0.0	B	0.01281	0.0	T	0.06607	-1.0817	10	0.35671	T	0.21	-14.8082	3.3956	0.07304	0.6396:0.1221:0.1201:0.1182	.	303	P53611	PGTB2_HUMAN	D	129;303	ENSP00000440452:E129D;ENSP00000317473:E303D	ENSP00000317473:E303D	E	+	3	2	RABGGTB	76032836	0.998000	0.40836	1.000000	0.80357	0.971000	0.66376	0.621000	0.24418	1.005000	0.39183	0.460000	0.39030	GAA	.	.	none		0.353	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582	
TNF	7124	hgsc.bcm.edu	37	6	31543607	31543607	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31543607G>A	ENST00000449264.2	+	1	264	c.89G>A	c.(88-90)tGc>tAc	p.C30Y		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	30					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	TCCAGGCGGTGCTTGTTCCTC	0.637									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.C30Y		Atlas-SNP	.											.	TNF	15	.	0			c.G89A						PASS	.						74.0	75.0	75.0					6																	31543607		2203	4300	6503	SO:0001583	missense	7124	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	GGCGGTGCTTGTT	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"""Tumor necrosis factor (ligand) superfamily"""	11892	protein-coding gene	gene with protein product	"""TNF superfamily, member 2"""	191160	"""tumor necrosis factor (TNF superfamily, member 2)"""	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.89G>A	6.37:g.31543607G>A	ENSP00000398698:p.Cys30Tyr	71.0	0.0	0		43.0	7.0	0.162791	NM_000594	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	37	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	G	9.575	1.122136	0.20877	.	.	ENSG00000232810	ENST00000449264	T	0.75589	-0.95	5.77	3.97	0.46021	.	0.369263	0.30252	N	0.010055	T	0.67599	0.2910	M	0.85945	2.785	0.09310	N	0.99999	P	0.38729	0.644	B	0.43658	0.426	T	0.64279	-0.6445	10	0.54805	T	0.06	.	8.8854	0.35400	0.0782:0.0:0.7725:0.1493	.	30	P01375	TNFA_HUMAN	Y	30	ENSP00000398698:C30Y	ENSP00000398698:C30Y	C	+	2	0	TNF	31651586	0.988000	0.35896	0.006000	0.13384	0.138000	0.21146	3.044000	0.49830	0.769000	0.33313	0.655000	0.94253	TGC	.	.	none		0.637	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2		
HBE1	3046	hgsc.bcm.edu	37	11	5289816	5289816	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5289816G>A	ENST00000380237.1	-	5	671	c.327C>T	c.(325-327)aaC>aaT	p.N109N	HBE1_ENST00000292896.2_Silent_p.N109N|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron			P02100	HBE_HUMAN	hemoglobin, epsilon 1	109					blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACCATCACGTTACCCAGGA	0.458																																					p.N109N		Atlas-SNP	.											.	HBE1	42	.	0			c.C327T						PASS	.						170.0	154.0	159.0					11																	5289816		2201	4298	6499	SO:0001819	synonymous_variant	3046	exon3			CATCACGTTACCC	BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675	ENST00000380237.1:c.327C>T	11.37:g.5289816G>A		49.0	0.0	0		54.0	6.0	0.111111	NM_005330	Q6FH44	Silent	SNP	ENST00000380237.1	37	CCDS7756.1																																																																																			.	.	none		0.458	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2	NM_005330	
NUDC	10726	hgsc.bcm.edu	37	1	27268110	27268110	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27268110A>C	ENST00000321265.5	+	3	445	c.322A>C	c.(322-324)Act>Cct	p.T108P		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	108					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		CAAGGAGCTAACTGATGAAGA	0.647																																					p.T108P		Atlas-SNP	.											.	NUDC	15	.	0			c.A322C						PASS	.						36.0	38.0	37.0					1																	27268110		2203	4299	6502	SO:0001583	missense	10726	exon3			GAGCTAACTGATG		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"""nuclear distribution gene C homolog (A. nidulans)"", ""nuclear distribution C homolog (A. nidulans)"""				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.322A>C	1.37:g.27268110A>C	ENSP00000319664:p.Thr108Pro	84.0	0.0	0		105.0	6.0	0.0571429	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	37	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.512255	0.85389	.	.	ENSG00000090273	ENST00000435827;ENST00000321265;ENST00000452707	T	0.42900	0.96	5.52	4.4	0.53042	.	0.045787	0.85682	D	0.000000	T	0.61986	0.2391	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.986	T	0.63980	-0.6514	10	0.48119	T	0.1	7.7528	10.843	0.46726	0.9265:0.0:0.0735:0.0	.	59;108	Q9H2R7;Q9Y266	.;NUDC_HUMAN	P	112;108;59	ENSP00000319664:T108P	ENSP00000319664:T108P	T	+	1	0	NUDC	27140697	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.283000	0.78640	2.111000	0.64477	0.533000	0.62120	ACT	.	.	none		0.647	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2		
EFCAB7	84455	hgsc.bcm.edu	37	1	64011657	64011657	+	Missense_Mutation	SNP	A	A	G	rs41313264	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:64011657A>G	ENST00000371088.4	+	7	1121	c.875A>G	c.(874-876)tAc>tGc	p.Y292C	DLEU2L_ENST00000371086.2_5'Flank|DLEU2L_ENST00000340052.3_5'Flank	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	292							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AGTCATCAGTACAGGATGCAA	0.333													A|||	9	0.00179712	0.0008	0.0043	5008	,	,		17625	0.0		0.004	False		,,,				2504	0.001				p.Y292C		Atlas-SNP	.											.	EFCAB7	45	.	0			c.A875G						PASS	.	A	CYS/TYR	8,4398	14.3+/-33.2	0,8,2195	96.0	96.0	96.0		875	5.8	1.0	1	dbSNP_127	96	93,8507	52.3+/-112.8	0,93,4207	yes	missense	EFCAB7	NM_032437.2	194	0,101,6402	GG,GA,AA		1.0814,0.1816,0.7766	probably-damaging	292/630	64011657	101,12905	2203	4300	6503	SO:0001583	missense	84455	exon7			ATCAGTACAGGAT	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.875A>G	1.37:g.64011657A>G	ENSP00000360129:p.Tyr292Cys	164.0	0.0	0		170.0	75.0	0.441176	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	21.5	4.164949	0.78339	0.001816	0.010814	ENSG00000203965	ENST00000371088	T	0.56444	0.46	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.66548	0.2800	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71570	-0.4553	10	0.87932	D	0	-9.1975	16.0742	0.80958	1.0:0.0:0.0:0.0	rs41313264;rs61744578	292	A8K855	EFCB7_HUMAN	C	292	ENSP00000360129:Y292C	ENSP00000360129:Y292C	Y	+	2	0	EFCAB7	63784245	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	6.808000	0.75206	2.204000	0.70986	0.482000	0.46254	TAC	A|0.993;G|0.007	0.007	strong		0.333	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
BTG2	7832	hgsc.bcm.edu	37	1	203274836	203274836	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274836G>A	ENST00000290551.4	+	1	173	c.102G>A	c.(100-102)agG>agA	p.R34R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCGAGCAGAGGCTTAAGGTCT	0.716																																					p.R34R		Atlas-SNP	.											.	BTG2	16	.	0			c.G102A						PASS	.						15.0	16.0	15.0					1																	203274836		2144	4202	6346	SO:0001819	synonymous_variant	7832	exon1			GCAGAGGCTTAAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.102G>A	1.37:g.203274836G>A		125.0	0.0	0		110.0	30.0	0.272727	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.716	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
HPSE2	60495	hgsc.bcm.edu	37	10	100481475	100481475	+	Missense_Mutation	SNP	C	C	T	rs142102360	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:100481475C>T	ENST00000370552.3	-	5	954	c.895G>A	c.(895-897)Gcc>Acc	p.A299T	HPSE2_ENST00000404542.1_Missense_Mutation_p.A187T|HPSE2_ENST00000370549.1_Missense_Mutation_p.A241T|HPSE2_ENST00000370546.1_Missense_Mutation_p.A299T	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	299					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		TATAAGCTGGCTCTGGAATAA	0.493													C|||	6	0.00119808	0.0	0.0014	5008	,	,		14180	0.0		0.004	False		,,,				2504	0.001				p.A299T		Atlas-SNP	.											.	HPSE2	203	.	0			c.G895A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	66.0	63.0	64.0		721,559,895,895	5.4	1.0	10	dbSNP_134	64	36,8564	25.1+/-72.6	0,36,4264	yes	missense,missense,missense,missense	HPSE2	NM_001166244.1,NM_001166245.1,NM_001166246.1,NM_021828.4	58,58,58,58	0,40,6463	TT,TC,CC		0.4186,0.0908,0.3076	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	241/535,187/481,299/549,299/593	100481475	40,12966	2203	4300	6503	SO:0001583	missense	60495	exon5			AGCTGGCTCTGGA	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.895G>A	10.37:g.100481475C>T	ENSP00000359583:p.Ala299Thr	61.0	0.0	0		52.0	21.0	0.403846	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	22.5	4.298050	0.81025	9.08E-4	0.004186	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.44	5.44	0.79542	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.062834	0.64402	D	0.000006	T	0.32010	0.0815	L	0.47016	1.485	0.58432	D	0.999996	P;P;P;P	0.51351	0.869;0.775;0.944;0.892	B;B;P;P	0.49421	0.38;0.356;0.572;0.61	T	0.02345	-1.1173	10	0.26408	T	0.33	-10.1813	14.4756	0.67544	0.147:0.853:0.0:0.0	.	187;299;241;299	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	T	299;241;299;187	ENSP00000359583:A299T;ENSP00000359580:A241T;ENSP00000359577:A299T;ENSP00000384384:A187T	ENSP00000359577:A299T	A	-	1	0	HPSE2	100471465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.129000	0.57957	2.706000	0.92434	0.551000	0.68910	GCC	C|0.997;T|0.003	0.003	strong		0.493	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
NPAS2	4862	hgsc.bcm.edu	37	2	101606810	101606810	+	Silent	SNP	G	G	A	rs1053091	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:101606810G>A	ENST00000335681.5	+	18	2205	c.1920G>A	c.(1918-1920)gcG>gcA	p.A640A	NPAS2_ENST00000542504.1_Silent_p.A705A	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	640					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCACAGCTGCGCTCCCGCCAA	0.617													G|||	52	0.0103834	0.0	0.0029	5008	,	,		14253	0.0		0.0278	False		,,,				2504	0.0225				p.A640A		Atlas-SNP	.											.	NPAS2	88	.	0			c.G1920A						PASS	.	G		16,4390	23.3+/-48.9	0,16,2187	50.0	53.0	52.0		1920	0.0	0.3	2	dbSNP_86	52	143,8457	71.3+/-133.9	1,141,4158	no	coding-synonymous	NPAS2	NM_002518.3		1,157,6345	AA,AG,GG		1.6628,0.3631,1.2225		640/825	101606810	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	4862	exon18			AGCTGCGCTCCCG	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1920G>A	2.37:g.101606810G>A		105.0	0.0	0		108.0	43.0	0.398148	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1	27	0.012362637362637362	0	0.0	1	0.0027624309392265192	0	0.0	26	0.03430079155672823	G	6.049	0.377437	0.11466	0.003631	0.016628	ENSG00000170485	ENST00000433408	T	0.42900	0.96	4.68	0.0241	0.14140	.	2.104730	0.02762	N	0.118661	T	0.14657	0.0354	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24190	-1.0167	7	0.44086	T	0.13	.	5.2335	0.15434	0.2565:0.2928:0.4506:0.0	rs1053091;rs3193576;rs1053091	.	.	.	T	139	ENSP00000393396:A139T	ENSP00000393396:A139T	A	+	1	0	NPAS2	100973242	0.014000	0.17966	0.293000	0.24932	0.101000	0.19017	0.173000	0.16724	0.368000	0.24481	-0.463000	0.05309	GCT	G|0.989;A|0.011	0.011	strong		0.617	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
MT-CO3	4514	hgsc.bcm.edu	37	M	9932	9932	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrM:9932G>A	ENST00000362079.2	+	1	726	c.726G>A	c.(724-726)tgG>tgA	p.W242*	MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS1_ENST00000387416.2_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	242					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						GCCTGATACTGGCATTTTGTA	0.383																																					p.W242W		Atlas-SNP	.											.	.	.	.	0			c.G726A						PASS	.																																			SO:0001587	stop_gained	5742	exon1			ATACTGGCATTTT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.726G>A	M.37:g.9932G>A	ENSP00000354982:p.Trp242*	4.0	0.0	0		8.0	8.0	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.383	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:169312974G>A	ENST00000305747.6	+	1	603	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	CERS6_ENST00000392687.4_Missense_Mutation_p.A6T	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	6					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGGGATCTTAGCCTGGTTCTG	0.657													G|||	39	0.00778754	0.0061	0.0101	5008	,	,		8564	0.0		0.0209	False		,,,				2504	0.0031				p.A6T		Atlas-SNP	.											.	.	.	.	0			c.G16A						PASS	.	G	THR/ALA	35,4371	40.0+/-72.8	2,31,2170	162.0	130.0	141.0		16	4.3	1.0	2	dbSNP_111	141	101,8499	56.4+/-117.6	0,101,4199	yes	missense	CERS6	NM_203463.1	58	2,132,6369	AA,AG,GG		1.1744,0.7944,1.0457	benign	6/385	169312974	136,12870	2203	4300	6503	SO:0001583	missense	253782	exon1			ATCTTAGCCTGGT	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"""Homeoboxes / CERS class"""	23826	protein-coding gene	gene with protein product		615336	"""LAG1 longevity assurance homolog 6 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 6"""	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.16G>A	2.37:g.169312974G>A	ENSP00000306579:p.Ala6Thr	75.0	0.0	0		72.0	36.0	0.5	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	24	0.01098901098901099	4	0.008130081300813009	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	21.6	4.173118	0.78452	0.007944	0.011744	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.21734	1.99;1.99	5.22	4.34	0.51931	.	0.105238	0.64402	N	0.000004	T	0.08358	0.0208	L	0.40543	1.245	0.58432	D	0.999999	B;B	0.32203	0.209;0.36	B;B	0.28465	0.045;0.09	T	0.04165	-1.0972	10	0.22706	T	0.39	-18.0462	13.4206	0.60996	0.0755:0.0:0.9245:0.0	.	6;6	Q32M63;Q6ZMG9	.;CERS6_HUMAN	T	6	ENSP00000306579:A6T;ENSP00000376453:A6T	ENSP00000306579:A6T	A	+	1	0	CERS6	169021220	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.346000	0.97056	1.188000	0.43014	0.467000	0.42956	GCC	A|0.008;G|0.990;T|0.002	0.008	strong		0.657	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463	
MASTL	84930	hgsc.bcm.edu	37	10	27462061	27462061	+	Silent	SNP	G	G	A	rs41282228	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27462061G>A	ENST00000375940.4	+	9	2196	c.2139G>A	c.(2137-2139)caG>caA	p.Q713Q	MASTL_ENST00000342386.6_Silent_p.Q712Q|MASTL_ENST00000375946.4_Silent_p.Q712Q|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	713	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCCAAATCAGATCAAGTCGG	0.438													G|||	50	0.00998403	0.0008	0.0029	5008	,	,		17354	0.0		0.0199	False		,,,				2504	0.0276				p.Q713Q		Atlas-SNP	.											.	MASTL	81	.	0			c.G2139A						PASS	.	G	,,	12,4394	19.1+/-41.9	0,12,2191	158.0	166.0	163.0		2139,2136,2136	1.3	0.0	10	dbSNP_127	163	151,8449	72.9+/-135.5	2,147,4151	no	coding-synonymous,coding-synonymous,coding-synonymous	MASTL	NM_001172303.1,NM_001172304.1,NM_032844.3	,,	2,159,6342	AA,AG,GG		1.7558,0.2724,1.2533	,,	713/880,712/841,712/879	27462061	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	84930	exon9			AAATCAGATCAAG	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.2139G>A	10.37:g.27462061G>A		52.0	0.0	0		66.0	31.0	0.469697	NM_001172303	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	37	CCDS53502.1																																																																																			G|0.989;A|0.011	0.011	strong		0.438	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
TUBGCP3	10426	hgsc.bcm.edu	37	13	113140350	113140350	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113140350C>T	ENST00000261965.3	-	22	2867	c.2681G>A	c.(2680-2682)cGt>cAt	p.R894H		NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	894					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					CAGAGACACACGGAGCCTGGG	0.582																																					p.R894H		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.G2681A						PASS	.						35.0	29.0	31.0					13																	113140350		2202	4295	6497	SO:0001583	missense	10426	exon22			GACACACGGAGCC	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"""spindle pole body protein"""					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.2681G>A	13.37:g.113140350C>T	ENSP00000261965:p.Arg894His	154.0	0.0	0		150.0	101.0	0.673333	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	37	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062569	0.55432	.	.	ENSG00000126216	ENST00000261965	T	0.24908	1.83	4.64	3.74	0.42951	.	0.060412	0.64402	N	0.000002	T	0.35682	0.0940	L	0.47716	1.5	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.56865	0.722;0.808	T	0.05115	-1.0905	10	0.45353	T	0.12	-11.4016	12.0433	0.53464	0.0:0.9099:0.0:0.0901	.	884;894	B4DYP7;Q96CW5	.;GCP3_HUMAN	H	894	ENSP00000261965:R894H	ENSP00000261965:R894H	R	-	2	0	TUBGCP3	112188351	0.999000	0.42202	0.028000	0.17463	0.268000	0.26511	4.824000	0.62701	0.964000	0.38108	-0.345000	0.07892	CGT	.	.	none		0.582	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322	
GDF9	2661	hgsc.bcm.edu	37	5	132200000	132200000	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:132200000A>C	ENST00000378673.2	-	2	1092	c.226T>G	c.(226-228)Tca>Gca	p.S76A	UQCRQ_ENST00000378670.3_5'Flank|GDF9_ENST00000296875.2_Missense_Mutation_p.S76A|UQCRQ_ENST00000378667.1_5'Flank|UQCRQ_ENST00000378665.1_5'Flank|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	76					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCCTAGGTGACCCACCTCGC	0.498																																					p.S76A		Atlas-SNP	.											.	GDF9	50	.	0			c.T226G						PASS	.						110.0	117.0	115.0					5																	132200000		2203	4300	6503	SO:0001583	missense	2661	exon1			TAGGTGACCCACC		CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"""Endogenous ligands"""	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.226T>G	5.37:g.132200000A>C	ENSP00000367942:p.Ser76Ala	95.0	0.0	0		100.0	13.0	0.13	NM_005260	Q4VAW5	Missense_Mutation	SNP	ENST00000378673.2	37	CCDS4162.1	.	.	.	.	.	.	.	.	.	.	A	4.388	0.071601	0.08436	.	.	ENSG00000164404	ENST00000378673;ENST00000296875	T;T	0.58506	0.33;0.33	5.92	-11.5	0.00074	.	1.261530	0.04922	N	0.455213	T	0.10680	0.0261	N	0.00138	-2.015	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07271	-1.0781	10	0.05436	T	0.98	.	2.0974	0.03671	0.2333:0.151:0.1436:0.472	.	76	O60383	GDF9_HUMAN	A	76	ENSP00000367942:S76A;ENSP00000296875:S76A	ENSP00000296875:S76A	S	-	1	0	GDF9	132227899	0.000000	0.05858	0.000000	0.03702	0.523000	0.34469	-1.884000	0.01622	-2.824000	0.00342	-0.132000	0.14878	TCA	.	.	none		0.498	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
DNAJA4	55466	hgsc.bcm.edu	37	15	78565495	78565495	+	Silent	SNP	G	G	A	rs74978019	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:78565495G>A	ENST00000394852.3	+	3	562	c.372G>A	c.(370-372)acG>acA	p.T124T	DNAJA4_ENST00000394855.3_Silent_p.T153T|DNAJA4_ENST00000446172.2_Silent_p.T97T|DNAJA4_ENST00000343789.3_Silent_p.T124T	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	124					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						ATGGAGTCACGAAGAAATTGG	0.348													G|||	6	0.00119808	0.0	0.0029	5008	,	,		18129	0.0		0.004	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											DNAJA4_ENST00000446172,NS,carcinoma,+1,2	DNAJA4	63	2	0			c.G459A						PASS	.	G	,,	3,4389	8.1+/-20.4	0,3,2193	92.0	97.0	96.0		372,291,459	-3.7	0.0	15	dbSNP_132	96	48,8538	29.6+/-80.5	0,48,4245	no	coding-synonymous,coding-synonymous,coding-synonymous	DNAJA4	NM_001130182.1,NM_001130183.1,NM_018602.3	,,	0,51,6438	AA,AG,GG		0.559,0.0683,0.393	,,	124/398,97/371,153/427	78565495	51,12927	2196	4293	6489	SO:0001819	synonymous_variant	55466	exon4			AGTCACGAAGAAA	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"""Heat shock proteins / DNAJ (HSP40)"""	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.372G>A	15.37:g.78565495G>A		234.0	1.0	0.0042735		255.0	113.0	0.443137	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	37	CCDS45316.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602	
SNX5	27131	hgsc.bcm.edu	37	20	17949050	17949050	+	Silent	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17949050A>G	ENST00000377768.3	-	2	331	c.19T>C	c.(19-21)Ttg>Ctg	p.L7L	MGME1_ENST00000377710.5_5'Flank|SNX5_ENST00000606602.1_Silent_p.L7L|SNX5_ENST00000481323.1_Silent_p.L7L|SNX5_ENST00000486039.1_Silent_p.L7L|MGME1_ENST00000377704.4_5'Flank|SNX5_ENST00000377759.4_Silent_p.L7L|MGME1_ENST00000377709.1_5'Flank|SNX5_ENST00000606557.1_Silent_p.L7L	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	7					intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						TGCTGCAGCAACTCGGGAACC	0.721																																					p.L7L		Atlas-SNP	.											SNX5,NS,lymphoid_neoplasm,+2,1	SNX5	38	1	0			c.T19C						scavenged	.						5.0	5.0	5.0					20																	17949050		1766	3420	5186	SO:0001819	synonymous_variant	27131	exon1			GCAGCAACTCGGG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.19T>C	20.37:g.17949050A>G		114.0	2.0	0.0175439		63.0	16.0	0.253968	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			.	.	none		0.721	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
BAI3	577	hgsc.bcm.edu	37	6	69348966	69348966	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:69348966A>C	ENST00000370598.1	+	3	1220	c.399A>C	c.(397-399)gtA>gtC	p.V133V		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	133	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TACGTCGAGTATTTCCAACTA	0.323																																					p.V133V		Atlas-SNP	.											BAI3,NS,carcinoma,+1,1	BAI3	451	1	0			c.A399C						scavenged	.						39.0	42.0	41.0					6																	69348966		2202	4300	6502	SO:0001819	synonymous_variant	577	exon3			TCGAGTATTTCCA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.399A>C	6.37:g.69348966A>C		36.0	0.0	0		43.0	9.0	0.209302	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			.	.	none		0.323	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
OR10J1	26476	hgsc.bcm.edu	37	1	159410258	159410258	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:159410258A>C	ENST00000423932.3	+	1	747	c.710A>C	c.(709-711)aAg>aCg	p.K237T	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	237					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|stomach(1)	25	all_hematologic(112;0.0429)					ACAATCCTCAAGATTGCTTCA	0.463																																					p.K237T		Atlas-SNP	.											OR10J1,NS,carcinoma,0,1	OR10J1	118	1	0			c.A710C						PASS	.						202.0	192.0	196.0					1																	159410258		2203	4300	6503	SO:0001583	missense	26476	exon1			TCCTCAAGATTGC	X64995	CCDS1185.1	1q23.2	2012-08-09			ENSG00000196184	ENSG00000196184		"""GPCR / Class A : Olfactory receptors"""	8175	protein-coding gene	gene with protein product						1370859	Standard	NM_012351		Approved	HGMP07J, HSHGMP07J	uc010piv.2	P30954	OTTHUMG00000022737	ENST00000423932.3:c.710A>C	1.37:g.159410258A>C	ENSP00000399078:p.Lys237Thr	229.0	0.0	0		226.0	69.0	0.30531	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Missense_Mutation	SNP	ENST00000423932.3	37	CCDS1185.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.867724	0.51588	.	.	ENSG00000196184	ENST00000423932	T	0.00169	8.63	4.29	0.577	0.17385	GPCR, rhodopsin-like superfamily (1);	0.159875	0.29239	N	0.012721	T	0.00144	0.0004	M	0.78637	2.42	0.09310	N	1	P	0.48503	0.911	P	0.56216	0.794	T	0.30238	-0.9985	10	0.87932	D	0	.	7.3103	0.26471	0.7181:0.0:0.2819:0.0	.	237	P30954	O10J1_HUMAN	T	237	ENSP00000399078:K237T	ENSP00000399078:K237T	K	+	2	0	OR10J1	157676882	0.000000	0.05858	0.216000	0.23742	0.957000	0.61999	0.008000	0.13197	-0.011000	0.14247	0.454000	0.30748	AAG	.	.	none		0.463	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351	
SGK1	6446	hgsc.bcm.edu	37	6	134494655	134494655	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494655G>A	ENST00000237305.7	-	4	366	c.278C>T	c.(277-279)gCt>gTt	p.A93V	SGK1_ENST00000528577.1_Missense_Mutation_p.A121V|SGK1_ENST00000413996.3_Missense_Mutation_p.A107V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.A83V|SGK1_ENST00000475719.2_Missense_Mutation_p.A93V|SGK1_ENST00000367858.5_Missense_Mutation_p.A188V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	93					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGATGGTTTAGCATGAGGATT	0.383																																					p.A188V		Atlas-SNP	.											.	SGK1	387	.	0			c.C563T						PASS	.						70.0	75.0	73.0					6																	134494655		2203	4300	6503	SO:0001583	missense	6446	exon6			GGTTTAGCATGAG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.278C>T	6.37:g.134494655G>A	ENSP00000237305:p.Ala93Val	81.0	0.0	0		85.0	16.0	0.188235	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826296	0.71143	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.71934	3.23;3.23;3.23;3.23;3.23;-0.61	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.74881	2.28	0.80722	D	1	P;D;B;B;P;B	0.56968	0.686;0.978;0.318;0.434;0.816;0.307	B;B;B;B;P;B	0.47915	0.272;0.39;0.176;0.175;0.561;0.085	T	0.66937	-0.5797	10	0.07813	T	0.8	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	121;107;93;83;188;93	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	188;107;93;83;121;93	ENSP00000356832:A188V;ENSP00000396242:A107V;ENSP00000237305:A93V;ENSP00000356831:A83V;ENSP00000434450:A121V;ENSP00000434302:A93V	ENSP00000237305:A93V	A	-	2	0	SGK1	134536348	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	GCT	.	.	none		0.383	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
LRRC16B	90668	hgsc.bcm.edu	37	14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	rs79328356	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24534916G>T	ENST00000342740.5	+	34	3636	c.3482G>T	c.(3481-3483)gGg>gTg	p.G1161V	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1161						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCCCTTCCCGGGTTGGAAAGA	0.617													G|||	98	0.0195687	0.003	0.0245	5008	,	,		17823	0.003		0.0616	False		,,,				2504	0.0123				p.G1161V		Atlas-SNP	.											LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	0			c.G3482T						PASS	.	G	VAL/GLY	63,4343	58.7+/-95.3	1,61,2141	123.0	109.0	114.0		3482	4.5	1.0	14	dbSNP_131	114	574,8026	154.6+/-208.8	26,522,3752	yes	missense	LRRC16B	NM_138360.3	109	27,583,5893	TT,TG,GG		6.6744,1.4299,4.8977	probably-damaging	1161/1373	24534916	637,12369	2203	4300	6503	SO:0001583	missense	90668	exon34			TTCCCGGGTTGGA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3482G>T	14.37:g.24534916G>T	ENSP00000340467:p.Gly1161Val	68.0	0.0	0		64.0	33.0	0.515625	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	G	18.54	3.645209	0.67358	0.014299	0.066744	ENSG00000186648	ENST00000342740	T	0.17854	2.25	5.4	4.51	0.55191	.	0.141061	0.33161	N	0.005214	T	0.01835	0.0058	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00950	-1.1503	10	0.72032	D	0.01	-15.7681	9.7564	0.40506	0.0947:0.0:0.9053:0.0	.	1161	Q8ND23	LR16B_HUMAN	V	1161	ENSP00000340467:G1161V	ENSP00000340467:G1161V	G	+	2	0	LRRC16B	23604756	0.964000	0.33143	0.972000	0.41901	0.867000	0.49689	1.806000	0.38892	1.272000	0.44329	0.655000	0.94253	GGG	G|0.958;T|0.042	0.042	strong		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
CSNK1A1	1452	hgsc.bcm.edu	37	5	148904609	148904609	+	Splice_Site	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148904609T>A	ENST00000377843.2	-	3	835	c.356A>T	c.(355-357)cAg>cTg	p.Q119L	CSNK1A1_ENST00000504676.1_Splice_Site_p.Q30L|CSNK1A1_ENST00000261798.5_Splice_Site_p.Q119L|CSNK1A1_ENST00000515435.1_Splice_Site_p.Q30L|CSNK1A1_ENST00000515768.1_Splice_Site_p.Q119L	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	119	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(4)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		TTCACATACCTGGTCAGCTAA	0.348																																					p.Q119L	Colon(5;64 69 1309 10383)	Atlas-SNP	.											.	CSNK1A1	63	.	0			c.A356T						PASS	.						63.0	61.0	62.0					5																	148904609		2080	4245	6325	SO:0001630	splice_region_variant	1452	exon3			CATACCTGGTCAG	AF119911	CCDS47303.1, CCDS47304.1, CCDS64291.1	5q32	2013-01-17			ENSG00000113712	ENSG00000113712			2451	protein-coding gene	gene with protein product	"""clock regulator kinase"""	600505				8050587	Standard	NM_001025105		Approved	CK1, CK1a, CK1alpha, CKIa, CKIalpha	uc003lqw.2	P48729	OTTHUMG00000163463	ENST00000377843.2:c.357+1A>T	5.37:g.148904609T>A		212.0	0.0	0		261.0	18.0	0.0689655	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Missense_Mutation	SNP	ENST00000377843.2	37	CCDS47303.1	.	.	.	.	.	.	.	.	.	.	T	31	5.103355	0.94245	.	.	ENSG00000113712	ENST00000261798;ENST00000377843;ENST00000504676;ENST00000515435;ENST00000322237;ENST00000515768	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	U	0.000000	T	0.73024	0.3534	H	0.99058	4.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0	D;D;D;D;D	0.83275	0.996;0.995;0.983;0.976;0.992	D	0.85007	0.0903	10	0.87932	D	0	.	15.9537	0.79865	0.0:0.0:0.0:1.0	.	30;119;119;119;30	B4DER9;Q71TU5;P48729;P48729-2;D6REM4	.;.;KC1A_HUMAN;.;.	L	119;119;30;30;119;119	ENSP00000261798:Q119L;ENSP00000367074:Q119L;ENSP00000426747:Q30L;ENSP00000427031:Q30L;ENSP00000421689:Q119L	ENSP00000261798:Q119L	Q	-	2	0	CSNK1A1	148884802	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	2.179000	0.69175	0.528000	0.53228	CAG	.	.	none		0.348	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892	Missense_Mutation
STRN3	29966	hgsc.bcm.edu	37	14	31404490	31404490	+	Silent	SNP	A	A	C	rs149753992		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31404490A>C	ENST00000357479.5	-	7	1063	c.867T>G	c.(865-867)gcT>gcG	p.A289A	STRN3_ENST00000355683.5_Silent_p.A289A|STRN3_ENST00000366206.2_5'Flank	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	289					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		TTAGGTCAGCAGCTAAACCTT	0.363																																					p.A289A		Atlas-SNP	.											.	STRN3	117	.	0			c.T867G						PASS	.	A	,	1,4405	2.1+/-5.4	0,1,2202	94.0	91.0	92.0		867,867	3.0	1.0	14	dbSNP_134	92	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	STRN3	NM_001083893.1,NM_014574.3	,	0,3,6500	CC,CA,AA		0.0233,0.0227,0.0231	,	289/798,289/714	31404490	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	29966	exon7			GTCAGCAGCTAAA		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.867T>G	14.37:g.31404490A>C		77.0	0.0	0		80.0	37.0	0.4625	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Silent	SNP	ENST00000357479.5	37	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	A	10.41	1.342669	0.24339	2.27E-4	2.33E-4	ENSG00000196792	ENST00000556577	.	.	.	5.68	2.98	0.34508	.	.	.	.	.	T	0.61553	0.2356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58769	-0.7578	4	.	.	.	-18.6432	11.3209	0.49421	0.6338:0.0:0.0:0.3662	.	.	.	.	G	50	.	.	C	-	1	0	STRN3	30474241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.814000	0.27239	0.940000	0.37473	0.459000	0.35465	TGC	A|1.000;C|0.000	0.000	weak		0.363	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
FAM53B	9679	hgsc.bcm.edu	37	10	126370517	126370517	+	Missense_Mutation	SNP	G	G	C	rs147832040		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:126370517G>C	ENST00000337318.3	-	4	776	c.565C>G	c.(565-567)Cga>Gga	p.R189G	RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000280780.6_Missense_Mutation_p.R189G|FAM53B_ENST00000392754.3_Missense_Mutation_p.R189G	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	189										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CCTCCAAATCGGTGGTGGAGT	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17444	0.0		0.0	False		,,,				2504	0.0				p.R189G		Atlas-SNP	.											.	FAM53B	22	.	0			c.C565G						PASS	.	G	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	34.0	37.0	36.0		565	2.5	0.0	10	dbSNP_134	36	23,8577	15.3+/-51.7	0,23,4277	yes	missense	FAM53B	NM_014661.3	125	0,24,6479	CC,CG,GG		0.2674,0.0227,0.1845	probably-damaging	189/423	126370517	24,12982	2203	4300	6503	SO:0001583	missense	9679	exon4			CAAATCGGTGGTG	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"""KIAA0140"""	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.565C>G	10.37:g.126370517G>C	ENSP00000338532:p.Arg189Gly	76.0	0.0	0		71.0	40.0	0.56338	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Missense_Mutation	SNP	ENST00000337318.3	37	CCDS7641.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	G	4.500	0.092832	0.08632	2.27E-4	0.002674	ENSG00000189319	ENST00000337318;ENST00000392754;ENST00000280780	T;T;T	0.45668	0.89;0.89;0.89	4.5	2.54	0.30619	.	0.743246	0.11858	N	0.522691	T	0.39733	0.1089	L	0.58101	1.795	0.09310	N	1	P;P;P	0.42620	0.6;0.785;0.6	B;B;B	0.43754	0.247;0.43;0.247	T	0.16217	-1.0410	10	0.13108	T	0.6	-3.0764	9.3857	0.38340	0.0:0.1397:0.5718:0.2884	.	189;189;189	Q14153-2;Q14153;B3KMZ2	.;FA53B_HUMAN;.	G	189	ENSP00000338532:R189G;ENSP00000376509:R189G;ENSP00000280780:R189G	ENSP00000280780:R189G	R	-	1	2	FAM53B	126360507	0.022000	0.18835	0.000000	0.03702	0.029000	0.11900	1.867000	0.39499	0.580000	0.29522	0.655000	0.94253	CGA	G|0.998;C|0.002	0.002	strong		0.667	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661	
DRC7	84229	hgsc.bcm.edu	37	16	57760115	57760115	+	Missense_Mutation	SNP	C	C	A	rs143054335	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57760115C>A	ENST00000360716.3	+	14	2115	c.1894C>A	c.(1894-1896)Cgc>Agc	p.R632S	CCDC135_ENST00000394337.4_Missense_Mutation_p.R632S|CCDC135_ENST00000336825.8_Missense_Mutation_p.R567S			Q8IY82	CC135_HUMAN		632					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)		p.R632C(1)		breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GGCCTCCAAGCGCGAGTTCCT	0.662													c|||	3	0.000599042	0.0	0.0	5008	,	,		17076	0.0		0.0	False		,,,				2504	0.0031				p.R632S		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	1	Substitution - Missense(1)	cervix(1)	c.C1894A						PASS	.	C	SER/ARG	0,4396		0,0,2198	68.0	61.0	63.0		1894	4.0	1.0	16	dbSNP_134	63	1,8595	1.2+/-3.3	0,1,4297	yes	missense	CCDC135	NM_032269.5	110	0,1,6495	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	632/875	57760115	1,12991	2198	4298	6496	SO:0001583	missense	84229	exon13			TCCAAGCGCGAGT																												ENST00000360716.3:c.1894C>A	16.37:g.57760115C>A	ENSP00000353942:p.Arg632Ser	157.0	0.0	0		154.0	64.0	0.415584	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	c	19.72	3.881029	0.72294	0.0	1.16E-4	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.14266	2.7;2.52;2.7	4.98	3.98	0.46160	.	0.278210	0.32884	N	0.005530	T	0.35008	0.0917	M	0.85630	2.765	0.33459	D	0.584648	D;D	0.76494	0.996;0.999	D;D	0.73380	0.95;0.98	T	0.51108	-0.8747	10	0.62326	D	0.03	-26.7085	6.3029	0.21123	0.3095:0.6029:0.0:0.0876	.	567;632	Q8IY82-2;Q8IY82	.;CC135_HUMAN	S	632;567;632	ENSP00000377869:R632S;ENSP00000338938:R567S;ENSP00000353942:R632S	ENSP00000338938:R567S	R	+	1	0	CCDC135	56317616	0.998000	0.40836	0.988000	0.46212	0.979000	0.70002	0.647000	0.24812	2.325000	0.78763	0.655000	0.94253	CGC	C|1.000;A|0.000	0.000	strong		0.662	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186121996C>T	ENST00000271588.4	+	96	15240	c.15011C>T	c.(15010-15012)aCt>aTt	p.T5004I	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTGAAGTCACTGTAAAGGTA	0.433													C|||	10	0.00199681	0.0	0.0014	5008	,	,		18553	0.0		0.008	False		,,,				2504	0.001				p.T5004I		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15011T						PASS	.	C	ILE/THR	4,4402	2.1+/-5.4	0,4,2199	196.0	170.0	179.0		15011	2.9	0.0	1	dbSNP_133	179	29,8571	9.1+/-34.3	1,27,4272	yes	missense	HMCN1	NM_031935.2	89	1,31,6471	TT,TC,CC		0.3372,0.0908,0.2537	benign	5004/5636	186121996	33,12973	2203	4300	6503	SO:0001583	missense	83872	exon96			AAGTCACTGTAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15011C>T	1.37:g.186121996C>T	ENSP00000271588:p.Thr5004Ile	156.0	0.0	0		168.0	72.0	0.428571	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.698	0.909113	0.17833	9.08E-4	0.003372	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31510	1.49;1.49	5.9	2.9	0.33743	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.27316	0.175	B	0.30855	0.121	T	0.34601	-0.9822	10	0.29301	T	0.29	.	9.0753	0.36517	0.4557:0.2514:0.2928:0.0	.	5004	Q96RW7	HMCN1_HUMAN	I	5004	ENSP00000271588:T5004I;ENSP00000356462:T5004I	ENSP00000271588:T5004I	T	+	2	0	HMCN1	184388619	0.000000	0.05858	0.026000	0.17262	0.758000	0.43043	0.220000	0.17660	0.314000	0.23086	0.650000	0.86243	ACT	C|0.996;T|0.004	0.004	strong		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CDH15	1013	hgsc.bcm.edu	37	16	89260195	89260195	+	Silent	SNP	G	G	A	rs62068507	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89260195G>A	ENST00000289746.2	+	13	2090	c.2025G>A	c.(2023-2025)ccG>ccA	p.P675P		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	675					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		TGCGTCACCCGACAGCGCTGA	0.706													G|||	16	0.00319489	0.0015	0.0029	5008	,	,		8843	0.0		0.0109	False		,,,				2504	0.001				p.P675P		Atlas-SNP	.											.	CDH15	54	.	0			c.G2025A						PASS	.	G		9,4279		0,9,2135	14.0	15.0	14.0		2025	-3.6	0.0	16	dbSNP_129	14	75,8425		0,75,4175	no	coding-synonymous	CDH15	NM_004933.2		0,84,6310	AA,AG,GG		0.8824,0.2099,0.6569		675/815	89260195	84,12704	2144	4250	6394	SO:0001819	synonymous_variant	1013	exon13			TCACCCGACAGCG	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2025G>A	16.37:g.89260195G>A		20.0	0.0	0		13.0	7.0	0.538462	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			G|0.995;A|0.005	0.005	strong		0.706	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
CRIP1	1396	hgsc.bcm.edu	37	14	105954687	105954687	+	Missense_Mutation	SNP	G	G	T	rs7824	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105954687G>T	ENST00000330233.7	+	3	1098	c.155G>T	c.(154-156)tGc>tTc	p.C52F	C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000392531.3_Missense_Mutation_p.C52F|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.C52F|C14orf80_ENST00000329886.7_5'Flank|CRIP1_ENST00000551180.1_Silent_p.L20L			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	52	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		AAACCCTACTGCAACCACCCC	0.652													G|||	11	0.00219649	0.0	0.0029	5008	,	,		10618	0.0		0.0089	False		,,,				2504	0.0				p.C52F		Atlas-SNP	.											.	CRIP1	1	.	0			c.G155T						PASS	.	G	PHE/CYS	11,4393	15.5+/-35.6	0,11,2191	46.0	63.0	57.0		155	3.8	1.0	14	dbSNP_52	57	105,8495	55.6+/-116.7	2,101,4197	yes	missense	CRIP1	NM_001311.4	205	2,112,6388	TT,TG,GG		1.2209,0.2498,0.892	probably-damaging	52/78	105954687	116,12888	2202	4300	6502	SO:0001583	missense	1396	exon4			CCTACTGCAACCA		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.155G>T	14.37:g.105954687G>T	ENSP00000332449:p.Cys52Phe	123.0	0.0	0		110.0	57.0	0.518182	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Missense_Mutation	SNP	ENST00000330233.7	37	CCDS10004.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	17.03	3.284634	0.59867	0.002498	0.012209	ENSG00000213145	ENST00000330233;ENST00000409393;ENST00000392531	D;D;D	0.99319	-5.74;-5.74;-5.74	4.76	3.8	0.43715	Zinc finger, LIM-type (4);	0.000000	0.56097	U	0.000022	D	0.98868	0.9617	.	.	.	0.58432	D	0.999998	D	0.56287	0.975	D	0.63192	0.912	D	0.95700	0.8748	9	0.87932	D	0	-12.7512	13.1083	0.59259	0.0:0.1623:0.8377:0.0	rs14079;rs11544873	52	P50238	CRIP1_HUMAN	F	52	ENSP00000332449:C52F;ENSP00000386340:C52F;ENSP00000376315:C52F	ENSP00000447493:C52F	C	+	2	0	CRIP1	105025732	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	8.181000	0.89696	2.186000	0.69663	0.650000	0.86243	TGC	C|0.064;G|0.923;T|0.013	0.013	strong		0.652	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311	
CLUL1	27098	hgsc.bcm.edu	37	18	618015	618015	+	Silent	SNP	C	C	G	rs116985056	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:618015C>G	ENST00000400606.2	+	2	160	c.15C>G	c.(13-15)ctC>ctG	p.L5L	CLUL1_ENST00000540035.1_Silent_p.L57L|CLUL1_ENST00000579494.1_Silent_p.L5L|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000581619.1_Silent_p.L30L|CLUL1_ENST00000338387.7_Silent_p.L5L	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	5					cell death (GO:0008219)	extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(5)|large_intestine(5)|liver(2)|lung(7)|ovary(2)|skin(1)	24						AGCCGCCACTCTTGGTGTTTA	0.438													C|||	2	0.000399361	0.0	0.0	5008	,	,		19800	0.0		0.001	False		,,,				2504	0.001				p.L5L		Atlas-SNP	.											.	CLUL1	57	.	0			c.C15G						PASS	.	C	,	2,3954		0,2,1976	110.0	111.0	111.0		15,15	2.3	0.6	18	dbSNP_132	111	21,8311		0,21,4145	no	coding-synonymous,coding-synonymous	CLUL1	NM_014410.4,NM_199167.1	,	0,23,6121	GG,GC,CC		0.252,0.0506,0.1872	,	5/467,5/467	618015	23,12265	1978	4166	6144	SO:0001819	synonymous_variant	27098	exon2			GCCACTCTTGGTG	D63813	CCDS42405.1, CCDS74187.1	18p11.32	2008-07-28				ENSG00000079101			2096	protein-coding gene	gene with protein product						10675623, 14507903	Standard	NM_199167		Approved		uc002kkq.3	Q15846		ENST00000400606.2:c.15C>G	18.37:g.618015C>G		109.0	0.0	0		91.0	30.0	0.32967	NM_199167	A0FDN7	Silent	SNP	ENST00000400606.2	37	CCDS42405.1																																																																																			C|0.999;G|0.001	0.001	strong		0.438	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1		
F2	2147	hgsc.bcm.edu	37	11	46751059	46751059	+	Silent	SNP	G	G	A	rs5900	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:46751059G>A	ENST00000311907.5	+	12	1658	c.1602G>A	c.(1600-1602)ccG>ccA	p.P534P	F2_ENST00000530231.1_Silent_p.P495P	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	534	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	TGGAGCGGCCGGTCTGCAAGG	0.627													G|||	37	0.00738818	0.0015	0.0173	5008	,	,		17598	0.0		0.0229	False		,,,				2504	0.0				p.P534P	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.G1602A						PASS	.	G		17,4385	24.3+/-50.5	1,15,2185	100.0	84.0	89.0		1602	-11.5	0.0	11	dbSNP_52	89	209,8389	89.7+/-151.9	1,207,4091	no	coding-synonymous	F2	NM_000506.3		2,222,6276	AA,AG,GG		2.4308,0.3862,1.7385		534/623	46751059	226,12774	2201	4299	6500	SO:0001819	synonymous_variant	2147	exon12			GCGGCCGGTCTGC	M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"""Endogenous ligands"""	3535	protein-coding gene	gene with protein product	"""prepro-coagulation factor II"""	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.1602G>A	11.37:g.46751059G>A		37.0	0.0	0		48.0	27.0	0.5625	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Silent	SNP	ENST00000311907.5	37	CCDS31476.1																																																																																			A|0.014;C|0.000;G|0.986	0.014	strong		0.627	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1		
FYCO1	79443	hgsc.bcm.edu	37	3	46008011	46008011	+	Missense_Mutation	SNP	C	C	G	rs531750827		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46008011C>G	ENST00000296137.2	-	8	3020	c.2815G>C	c.(2815-2817)Gca>Cca	p.A939P	FYCO1_ENST00000535325.1_Missense_Mutation_p.A939P	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	939					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTTGAGGCTGCCTCTTTGGCG	0.632																																					p.A939P		Atlas-SNP	.											.	FYCO1	115	.	0			c.G2815C						PASS	.						60.0	59.0	59.0					3																	46008011		2203	4300	6503	SO:0001583	missense	79443	exon8			AGGCTGCCTCTTT	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2815G>C	3.37:g.46008011C>G	ENSP00000296137:p.Ala939Pro	147.0	0.0	0		135.0	71.0	0.525926	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	6.021	0.372341	0.11409	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79352	-1.26;-1.26	5.39	3.35	0.38373	.	1.014420	0.07877	N	0.968878	T	0.71962	0.3402	L	0.51422	1.61	0.25832	N	0.984155	P;P	0.47604	0.883;0.898	B;P	0.44477	0.346;0.451	T	0.61466	-0.7057	10	0.37606	T	0.19	-1.0259	3.3906	0.07287	0.0:0.455:0.2375:0.3074	.	939;939	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	P	939	ENSP00000296137:A939P;ENSP00000441178:A939P	ENSP00000296137:A939P	A	-	1	0	FYCO1	45983015	0.139000	0.22563	0.594000	0.28785	0.047000	0.14425	0.695000	0.25527	1.289000	0.44618	-0.136000	0.14681	GCA	.	.	none		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
BAZ2B	29994	hgsc.bcm.edu	37	2	160182374	160182374	+	Missense_Mutation	SNP	T	T	C	rs148382881	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:160182374T>C	ENST00000392783.2	-	35	6494	c.5999A>G	c.(5998-6000)aAt>aGt	p.N2000S	BAZ2B_ENST00000355831.2_Missense_Mutation_p.N1966S|BAZ2B_ENST00000392782.1_Missense_Mutation_p.N1964S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.N1900S	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	2000					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTTTGACTCATTAGTCTTTTT	0.328													T|||	30	0.00599042	0.0015	0.0173	5008	,	,		16283	0.001		0.0149	False		,,,				2504	0.0				p.N2000S		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A5999G						PASS	.	T	SER/ASN	13,3637		0,13,1812	99.0	90.0	93.0		5999	3.7	0.9	2	dbSNP_134	93	136,8022		3,130,3946	yes	missense	BAZ2B	NM_013450.2	46	3,143,5758	CC,CT,TT		1.6671,0.3562,1.2619	benign	2000/2169	160182374	149,11659	1825	4079	5904	SO:0001583	missense	29994	exon35			GACTCATTAGTCT	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.5999A>G	2.37:g.160182374T>C	ENSP00000376534:p.Asn2000Ser	132.0	0.0	0		103.0	20.0	0.194175	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	15	0.006868131868131868	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	5	0.006596306068601583	T	9.716	1.158442	0.21454	0.003562	0.016671	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.83	3.66	0.41972	.	0.000000	0.36972	U	0.002312	T	0.18257	0.0438	L	0.27053	0.805	0.28931	N	0.891542	B;B	0.24768	0.111;0.016	B;B	0.23574	0.047;0.006	T	0.12553	-1.0543	10	0.15952	T	0.53	-12.5921	5.4583	0.16602	0.0:0.1583:0.1464:0.6953	.	1964;2000	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	S	1964;2000;1966;1900	ENSP00000376533:N1964S;ENSP00000376534:N2000S;ENSP00000348087:N1966S;ENSP00000339670:N1900S	ENSP00000339670:N1900S	N	-	2	0	BAZ2B	159890620	0.976000	0.34144	0.938000	0.37757	0.998000	0.95712	0.748000	0.26305	0.696000	0.31696	0.454000	0.30748	AAT	T|0.987;C|0.013	0.013	strong		0.328	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
EPPK1	83481	hgsc.bcm.edu	37	8	144942794	144942794	+	Missense_Mutation	SNP	G	G	A	rs373737061	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144942794G>A	ENST00000525985.1	-	2	4699	c.4628C>T	c.(4627-4629)aCg>aTg	p.T1543M				P58107	EPIPL_HUMAN	epiplakin 1	1543						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTCGTCCAGCGTCTTCCTGCT	0.647													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		20163	0.001		0.002	False		,,,				2504	0.0				p.T1543M		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.C4628T						PASS	.	G	MET/THR	0,4186		0,0,2093	20.0	22.0	22.0		4628	2.6	0.1	8		22	3,8413		0,3,4205	no	missense	EPPK1	NM_031308.1	81	0,3,6298	AA,AG,GG		0.0356,0.0,0.0238	probably-damaging	1543/2420	144942794	3,12599	2093	4208	6301	SO:0001583	missense	83481	exon1			TCCAGCGTCTTCC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4628C>T	8.37:g.144942794G>A	ENSP00000436337:p.Thr1543Met	66.0	0.0	0		82.0	44.0	0.536585	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	G	10.52	1.373843	0.24857	0.0	3.56E-4	ENSG00000227184	ENST00000525985	T	0.70986	-0.53	4.41	2.62	0.31277	.	.	.	.	.	T	0.77844	0.4191	L	0.49455	1.56	0.19945	N	0.999945	D	0.89917	1.0	D	0.91635	0.999	T	0.64706	-0.6344	9	0.72032	D	0.01	.	8.5002	0.33152	0.192:0.0:0.808:0.0	.	1543	E9PPU0	.	M	1543	ENSP00000436337:T1543M	ENSP00000436337:T1543M	T	-	2	0	EPPK1	145014782	0.117000	0.22190	0.131000	0.22000	0.300000	0.27592	1.414000	0.34736	0.497000	0.27926	-0.218000	0.12543	ACG	.	.	weak		0.647	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
GALNT8	26290	hgsc.bcm.edu	37	12	4854722	4854722	+	Missense_Mutation	SNP	G	G	A	rs201387598		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4854722G>A	ENST00000252318.2	+	5	1325	c.988G>A	c.(988-990)Gaa>Aaa	p.E330K		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	330					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GTTTAACTGGGAACTCTGGTG	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		21588	0.0		0.001	False		,,,				2504	0.0				p.E330K	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.G988A						PASS	.						117.0	99.0	105.0					12																	4854722		2203	4300	6503	SO:0001583	missense	26290	exon5			AACTGGGAACTCT	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.988G>A	12.37:g.4854722G>A	ENSP00000252318:p.Glu330Lys	111.0	0.0	0		94.0	43.0	0.457447	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	G	6.158	0.397270	0.11638	.	.	ENSG00000130035	ENST00000252318	T	0.59638	0.25	4.2	-3.18	0.05186	.	0.312551	0.29699	N	0.011436	T	0.23649	0.0572	N	0.04090	-0.28	0.18873	N	0.999986	B	0.13145	0.007	B	0.16289	0.015	T	0.18713	-1.0328	10	0.15066	T	0.55	.	5.2053	0.15287	0.3905:0.2669:0.3426:0.0	.	330	Q9NY28	GALT8_HUMAN	K	330	ENSP00000252318:E330K	ENSP00000252318:E330K	E	+	1	0	GALNT8	4724983	0.924000	0.31332	0.017000	0.16124	0.784000	0.44337	1.344000	0.33941	-0.510000	0.06523	-0.479000	0.04858	GAA	G|0.999;A|0.001	0.001	weak		0.488	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
PDCD11	22984	hgsc.bcm.edu	37	10	105160184	105160184	+	Missense_Mutation	SNP	A	A	G	rs150893869	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105160184A>G	ENST00000369797.3	+	3	227	c.133A>G	c.(133-135)Aaa>Gaa	p.K45E		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	45					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CACCAAAAGAAAAAAGAGCCA	0.423													A|||	103	0.0205671	0.0	0.0086	5008	,	,		13928	0.002		0.006	False		,,,				2504	0.091				p.K45E		Atlas-SNP	.											.	PDCD11	160	.	0			c.A133G						PASS	.	A	GLU/LYS	3,4403	9.9+/-24.2	0,3,2200	57.0	66.0	63.0		133	5.8	1.0	10	dbSNP_134	63	54,8546	32.3+/-84.9	0,54,4246	yes	missense	PDCD11	NM_014976.1	56	0,57,6446	GG,GA,AA		0.6279,0.0681,0.4383	probably-damaging	45/1872	105160184	57,12949	2203	4300	6503	SO:0001583	missense	22984	exon3			AAAAGAAAAAAGA	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.133A>G	10.37:g.105160184A>G	ENSP00000358812:p.Lys45Glu	23.0	0.0	0		17.0	10.0	0.588235	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	27.6	4.844336	0.91197	6.81E-4	0.006279	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.14391	2.51	5.84	5.84	0.93424	.	0.235564	0.45606	D	0.000344	T	0.21307	0.0513	M	0.64404	1.975	0.51012	D	0.999903	D	0.58620	0.983	P	0.54815	0.761	T	0.00621	-1.1640	10	0.87932	D	0	-6.4297	14.4461	0.67349	1.0:0.0:0.0:0.0	.	45	Q14690	RRP5_HUMAN	E	45	ENSP00000358812:K45E	ENSP00000358812:K45E	K	+	1	0	PDCD11	105150174	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.140000	0.64807	2.235000	0.73313	0.459000	0.35465	AAA	A|0.995;G|0.005	0.005	strong		0.423	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
TLN2	83660	hgsc.bcm.edu	37	15	63131091	63131091	+	Missense_Mutation	SNP	C	C	T	rs140301741	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:63131091C>T	ENST00000561311.1	+	57	7641	c.7411C>T	c.(7411-7413)Ctt>Ttt	p.L2471F	TLN2_ENST00000306829.6_Missense_Mutation_p.L2471F|RP11-1069G10.1_ENST00000558404.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2471	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CTCAGACAATCTTGTCCGTGC	0.458													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21391	0.0		0.002	False		,,,				2504	0.0				p.L2471F		Atlas-SNP	.											.	TLN2	253	.	0			c.C7411T						PASS	.	C	PHE/LEU	2,4404	6.2+/-15.9	0,2,2201	115.0	108.0	110.0		7411	5.7	1.0	15	dbSNP_134	110	33,8567	23.4+/-69.3	0,33,4267	yes	missense	TLN2	NM_015059.2	22	0,35,6468	TT,TC,CC		0.3837,0.0454,0.2691	probably-damaging	2471/2543	63131091	35,12971	2203	4300	6503	SO:0001583	missense	83660	exon55			GACAATCTTGTCC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7411C>T	15.37:g.63131091C>T	ENSP00000453508:p.Leu2471Phe	62.0	0.0	0		58.0	31.0	0.534483	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	32	5.128337	0.94473	4.54E-4	0.003837	ENSG00000171914	ENST00000306829	T	0.60548	0.18	5.68	5.68	0.88126	I/LWEQ (4);	0.000000	0.85682	D	0.000000	D	0.83326	0.5230	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.995;1.0	D	0.87137	0.2200	10	0.87932	D	0	-10.4216	19.786	0.96437	0.0:1.0:0.0:0.0	.	87;2471	B4DGF3;Q9Y4G6	.;TLN2_HUMAN	F	2471	ENSP00000303476:L2471F	ENSP00000303476:L2471F	L	+	1	0	TLN2	60918144	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	2.676000	0.91093	0.563000	0.77884	CTT	C|0.998;T|0.002	0.002	strong		0.458	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84.0	83.0	83.0					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	15.0	0.0	0		23.0	2.0	0.0869565	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
LEMD3	23592	hgsc.bcm.edu	37	12	65563416	65563416	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:65563416G>A	ENST00000308330.2	+	1	66	c.40G>A	c.(40-42)Gat>Aat	p.D14N	LEMD3_ENST00000541171.1_3'UTR	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	14	LEM. {ECO:0000255|PROSITE- ProRule:PRU00313}.				negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		GCAGCTCTCGGATGAGGAGCT	0.627																																					p.D14N		Atlas-SNP	.											.	LEMD3	68	.	0			c.G40A						PASS	.						11.0	10.0	10.0					12																	65563416		2180	4271	6451	SO:0001583	missense	23592	exon1			CTCTCGGATGAGG	AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.40G>A	12.37:g.65563416G>A	ENSP00000308369:p.Asp14Asn	66.0	0.0	0		63.0	9.0	0.142857	NM_001167614	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	37	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823509	0.90873	.	.	ENSG00000174106	ENST00000308330	T	0.61274	0.12	3.98	3.98	0.46160	LEM-like domain (2);Lamino-associated polypeptide 2/emerin (3);	0.000000	0.85682	D	0.000000	T	0.59500	0.2198	N	0.20401	0.57	0.52501	D	0.999955	D;D	0.63046	0.992;0.992	D;D	0.64776	0.929;0.929	T	0.58132	-0.7690	9	.	.	.	-14.3277	16.0229	0.80512	0.0:0.0:1.0:0.0	.	14;14	B4E2K7;Q9Y2U8	.;MAN1_HUMAN	N	14	ENSP00000308369:D14N	.	D	+	1	0	LEMD3	63849683	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.246000	0.89828	2.501000	0.84356	0.462000	0.41574	GAT	.	.	none		0.627	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2		
USH1C	10083	hgsc.bcm.edu	37	11	17527386	17527386	+	Intron	SNP	A	A	G	rs369021714		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17527386A>G	ENST00000318024.4	-	16	1393				USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000005226.7_Silent_p.S708S|USH1C_ENST00000527020.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CCAGAACTTCAGATTTCACAG	0.592																																					p.S708S		Atlas-SNP	.											.	USH1C	157	.	0			c.T2124C						PASS	.	A	,	0,4400		0,0,2200	59.0	59.0	59.0		,2124	-10.4	0.2	11		59	1,8585	1.2+/-3.3	0,1,4292	no	intron,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	0,1,6492	GG,GA,AA		0.0116,0.0,0.0077	,	,708/900	17527386	1,12985	2200	4293	6493	SO:0001627	intron_variant	10083	exon19			AACTTCAGATTTC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1285-3859T>C	11.37:g.17527386A>G		74.0	0.0	0		80.0	41.0	0.5125	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			.	.	weak		0.592	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
CD109	135228	hgsc.bcm.edu	37	6	74481186	74481186	+	Missense_Mutation	SNP	C	C	T	rs41266745	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:74481186C>T	ENST00000287097.5	+	15	1821	c.1709C>T	c.(1708-1710)cCa>cTa	p.P570L	CD109_ENST00000437994.2_Missense_Mutation_p.P570L|CD109_ENST00000422508.2_Missense_Mutation_p.P493L			Q6YHK3	CD109_HUMAN	CD109 molecule	570					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AAAGCTGAACCATCTGAGAAA	0.368													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18121	0.0		0.001	False		,,,				2504	0.001				p.P570L		Atlas-SNP	.											.	CD109	170	.	0			c.C1709T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	9,4397	15.5+/-35.6	1,7,2195	94.0	90.0	92.0		1709,1478,1709	4.6	0.9	6	dbSNP_127	92	35,8565	24.6+/-71.5	0,35,4265	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	98,98,98	1,42,6460	TT,TC,CC		0.407,0.2043,0.3383	probably-damaging,probably-damaging,probably-damaging	570/1429,493/1369,570/1446	74481186	44,12962	2203	4300	6503	SO:0001583	missense	135228	exon15			CTGAACCATCTGA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.1709C>T	6.37:g.74481186C>T	ENSP00000287097:p.Pro570Leu	57.0	0.0	0		43.0	23.0	0.534884	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.80	2.940037	0.52972	0.002043	0.00407	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.79554	-1.28;-1.28;-1.28	5.5	4.64	0.57946	Alpha-2-macroglobulin, N-terminal 2 (1);	0.000000	0.85682	D	0.000000	D	0.88851	0.6549	M	0.88570	2.965	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.935;0.999;0.999;0.998	D	0.91181	0.4976	10	0.87932	D	0	.	13.4261	0.61026	0.0:0.9239:0.0:0.0761	rs41266745	493;570;570;570	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	L	570;493;570	ENSP00000388062:P570L;ENSP00000404475:P493L;ENSP00000287097:P570L	ENSP00000287097:P570L	P	+	2	0	CD109	74537907	1.000000	0.71417	0.884000	0.34674	0.286000	0.27126	4.749000	0.62155	1.567000	0.49668	0.655000	0.94253	CCA	C|0.998;T|0.002	0.002	strong		0.368	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
FRMD1	79981	hgsc.bcm.edu	37	6	168458002	168458002	+	Silent	SNP	G	G	A	rs55991596	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:168458002G>A	ENST00000283309.6	-	11	1489	c.1425C>T	c.(1423-1425)gcC>gcT	p.A475A	FRMD1_ENST00000440994.2_Silent_p.A407A|FRMD1_ENST00000537786.1_Silent_p.A246A|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	475						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CACTGACCCCGGCTGTCATTT	0.657													G|||	107	0.0213658	0.003	0.0403	5008	,	,		17366	0.0		0.0666	False		,,,				2504	0.0082				p.A475A	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C1425T						PASS	.	G	,	55,4351	52.9+/-88.7	0,55,2148	30.0	29.0	29.0		1221,1425	-0.1	0.0	6	dbSNP_129	29	548,8052	142.0+/-198.3	14,520,3766	no	coding-synonymous,coding-synonymous	FRMD1	NM_001122841.1,NM_024919.3	,	14,575,5914	AA,AG,GG		6.3721,1.2483,4.6363	,	407/482,475/550	168458002	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	79981	exon11			GACCCCGGCTGTC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1425C>T	6.37:g.168458002G>A		77.0	0.0	0		72.0	37.0	0.513889	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.958;A|0.042	0.042	strong		0.657	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
LARS	51520	hgsc.bcm.edu	37	5	145522992	145522992	+	Silent	SNP	C	C	T	rs146906828	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:145522992C>T	ENST00000394434.2	-	19	2026	c.1860G>A	c.(1858-1860)gaG>gaA	p.E620E	LARS_ENST00000545646.1_Silent_p.E574E|LARS_ENST00000510191.1_Silent_p.E566E|LARS_ENST00000274562.9_Silent_p.E593E	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	620					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CCAGCGGAGACTCTGCCTGTC	0.393													C|||	2	0.000399361	0.0	0.0	5008	,	,		13876	0.002		0.0	False		,,,				2504	0.0				p.E620E		Atlas-SNP	.											.	LARS	100	.	0			c.G1860A						PASS	.	C		0,4406		0,0,2203	196.0	195.0	195.0		1860	-2.7	1.0	5	dbSNP_134	195	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	LARS	NM_020117.9		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		620/1177	145522992	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon19			CGGAGACTCTGCC	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.1860G>A	5.37:g.145522992C>T		79.0	0.0	0		88.0	45.0	0.511364	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			C|0.997;T|0.003	0.003	strong		0.393	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
CARD14	79092	hgsc.bcm.edu	37	17	78157961	78157961	+	Missense_Mutation	SNP	G	G	A	rs114688446	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78157961G>A	ENST00000573882.1	+	6	1135	c.599G>A	c.(598-600)aGc>aAc	p.S200N	CARD14_ENST00000392434.2_5'Flank|CARD14_ENST00000344227.2_Missense_Mutation_p.S200N|CARD14_ENST00000570421.1_Missense_Mutation_p.S200N			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	200			S -> N (in dbSNP:rs114688446). {ECO:0000269|PubMed:22521419}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GAGATGCTCAGCCTCTCGCTG	0.652													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18540	0.0		0.002	False		,,,				2504	0.0072				p.S200N		Atlas-SNP	.											.	CARD14	98	.	0			c.G599A						PASS	.						28.0	21.0	24.0					17																	78157961		2186	4282	6468	SO:0001583	missense	79092	exon4			TGCTCAGCCTCTC	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.599G>A	17.37:g.78157961G>A	ENSP00000458715:p.Ser200Asn	68.0	0.0	0		73.0	34.0	0.465753	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	0.004	-2.372545	0.00209	.	.	ENSG00000141527	ENST00000344227	T	0.34072	1.38	3.58	-3.66	0.04489	.	0.717962	0.13758	N	0.364763	T	0.06735	0.0172	N	0.02916	-0.46	0.19945	N	0.999944	B	0.02656	0.0	B	0.04013	0.001	T	0.32214	-0.9915	10	0.02654	T	1	-3.1167	5.8528	0.18701	0.5403:0.1435:0.3162:0.0	.	200	Q9BXL6	CAR14_HUMAN	N	200	ENSP00000344549:S200N	ENSP00000344549:S200N	S	+	2	0	CARD14	75772556	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	-0.119000	0.10676	-0.492000	0.06687	-0.479000	0.04858	AGC	A|0.001;G|0.994;T|0.005	0.001	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
RGS1	5996	hgsc.bcm.edu	37	1	192545417	192545417	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:192545417G>A	ENST00000367459.3	+	2	206	c.140G>A	c.(139-141)gGa>gAa	p.G47E	RGS1_ENST00000469578.2_Missense_Mutation_p.G47E	NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	47					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				TTTTGTAGTGGAATGGATATG	0.308																																					p.G47E		Atlas-SNP	.											.	RGS1	75	.	0			c.G140A						PASS	.						70.0	72.0	71.0					1																	192545417		2203	4297	6500	SO:0001583	missense	5996	exon2			GTAGTGGAATGGA	AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"""Regulators of G-protein signaling"""	9991	protein-coding gene	gene with protein product		600323	"""regulator of G-protein signalling 1"""	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.140G>A	1.37:g.192545417G>A	ENSP00000356429:p.Gly47Glu	182.0	0.0	0		178.0	43.0	0.241573	NM_002922	B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	ENST00000367459.3	37	CCDS1375.2	.	.	.	.	.	.	.	.	.	.	G	13.06	2.124692	0.37533	.	.	ENSG00000090104	ENST00000367459	T	0.37584	1.19	6.17	6.17	0.99709	.	0.241459	0.36002	N	0.002853	T	0.47525	0.1450	L	0.29908	0.895	0.43084	D	0.994743	D;B	0.76494	0.999;0.149	D;B	0.72075	0.976;0.032	T	0.26985	-1.0087	10	0.38643	T	0.18	.	14.9828	0.71324	0.0:0.1422:0.8578:0.0	.	47;47	Q08116-2;Q08116	.;RGS1_HUMAN	E	47	ENSP00000356429:G47E	ENSP00000356429:G47E	G	+	2	0	RGS1	190812040	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.974000	0.56852	2.941000	0.99782	0.655000	0.94253	GGA	.	.	none		0.308	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922	
TULP4	56995	hgsc.bcm.edu	37	6	158923378	158923378	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158923378G>A	ENST00000367097.3	+	13	4040	c.2683G>A	c.(2683-2685)Ggc>Agc	p.G895S	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	895					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CGACAGCAGTGGCAACGTGGA	0.637																																					p.G895S		Atlas-SNP	.											.	TULP4	137	.	0			c.G2683A						PASS	.						68.0	72.0	71.0					6																	158923378		2203	4300	6503	SO:0001583	missense	56995	exon13			AGCAGTGGCAACG		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2683G>A	6.37:g.158923378G>A	ENSP00000356064:p.Gly895Ser	87.0	0.0	0		82.0	4.0	0.0487805	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.940588	0.92526	.	.	ENSG00000130338	ENST00000367097	T	0.75589	-0.95	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.83202	0.5203	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85241	0.1038	10	0.87932	D	0	-33.3275	18.5327	0.90999	0.0:0.0:1.0:0.0	.	895	Q9NRJ4	TULP4_HUMAN	S	895	ENSP00000356064:G895S	ENSP00000356064:G895S	G	+	1	0	TULP4	158843366	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.894000	0.92506	2.379000	0.81126	0.561000	0.74099	GGC	.	.	none		0.637	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
CCDC80	151887	hgsc.bcm.edu	37	3	112356977	112356977	+	Silent	SNP	T	T	C	rs35149092	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112356977T>C	ENST00000206423.3	-	2	2729	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	CCDC80_ENST00000439685.2_Silent_p.E592E|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	592	Lys-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						AGCCATCCTGTTCTGTTTTAC	0.448													T|||	10	0.00199681	0.0	0.0101	5008	,	,		19219	0.0		0.003	False		,,,				2504	0.0				p.E592E		Atlas-SNP	.											.	CCDC80	100	.	0			c.A1776G						PASS	.	T	,	3,4403	6.2+/-15.9	0,3,2200	260.0	241.0	247.0		1776,1776	4.1	1.0	3	dbSNP_126	247	28,8572	20.4+/-63.3	0,28,4272	no	coding-synonymous,coding-synonymous	CCDC80	NM_199511.1,NM_199512.1	,	0,31,6472	CC,CT,TT		0.3256,0.0681,0.2384	,	592/951,592/951	112356977	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	151887	exon2			ATCCTGTTCTGTT	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1776A>G	3.37:g.112356977T>C		239.0	0.0	0		233.0	116.0	0.497854	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	37	CCDS2968.1																																																																																			T|0.996;C|0.004	0.004	strong		0.448	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
DPCR1	135656	hgsc.bcm.edu	37	6	30919798	30919798	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30919798A>C	ENST00000462446.1	+	2	3585	c.3557A>C	c.(3556-3558)aAg>aCg	p.K1186T	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.K28T			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	314						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						ACCCCAGAAAAGCCTACGCTA	0.473																																					p.K1186T		Atlas-SNP	.											.	DPCR1	99	.	0			c.A3557C						PASS	.						161.0	160.0	161.0					6																	30919798		2203	4300	6503	SO:0001583	missense	135656	exon2			CAGAAAAGCCTAC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3557A>C	6.37:g.30919798A>C	ENSP00000417182:p.Lys1186Thr	25.0	0.0	0		45.0	16.0	0.355556	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	A	9.633	1.137016	0.21123	.	.	ENSG00000168631	ENST00000462446;ENST00000304311	T;T	0.26518	1.73;1.75	1.6	0.339	0.15979	.	.	.	.	.	T	0.15176	0.0366	L	0.59436	1.845	0.09310	N	1	D	0.62365	0.991	P	0.53401	0.725	T	0.07616	-1.0763	9	0.31617	T	0.26	.	5.0167	0.14339	0.7344:0.0:0.0:0.2656	.	1186	E9PEI6	.	T	1186;28	ENSP00000417182:K1186T;ENSP00000305948:K28T	ENSP00000305948:K28T	K	+	2	0	DPCR1	31027777	0.000000	0.05858	0.002000	0.10522	0.149000	0.21700	-1.215000	0.02985	0.066000	0.16515	-0.737000	0.03537	AAG	.	.	none		0.473	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
KTN1	3895	hgsc.bcm.edu	37	14	56119783	56119783	+	Missense_Mutation	SNP	G	G	A	rs139730003		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:56119783G>A	ENST00000395314.3	+	27	2811	c.2743G>A	c.(2743-2745)Gca>Aca	p.A915T	Y_RNA_ENST00000363872.1_RNA|KTN1_ENST00000416613.1_Missense_Mutation_p.A915T|KTN1_ENST00000438792.2_Missense_Mutation_p.A915T|KTN1_ENST00000395309.3_Missense_Mutation_p.A915T|KTN1_ENST00000395308.1_Missense_Mutation_p.A892T|KTN1_ENST00000395311.1_Missense_Mutation_p.A892T|KTN1_ENST00000554507.1_Missense_Mutation_p.A210T|KTN1_ENST00000413890.2_Missense_Mutation_p.A892T	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	915					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TCAGGAAGTAGCACAACATAA	0.274			T	RET	papillary thryoid																																p.A915T		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G2743A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4404		0,0,2202	325.0	348.0	340.0		2743,2674,2743,2743	1.3	0.4	14	dbSNP_134	340	4,8574	3.7+/-12.6	0,4,4285	yes	missense,missense,missense,missense	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	58,58,58,58	0,4,6487	AA,AG,GG		0.0466,0.0,0.0308	benign,benign,benign,benign	915/1358,892/1307,915/1301,915/1358	56119783	4,12978	2202	4289	6491	SO:0001583	missense	3895	exon27			GAAGTAGCACAAC		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2743G>A	14.37:g.56119783G>A	ENSP00000378725:p.Ala915Thr	154.0	0.0	0		163.0	75.0	0.460123	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	8.195	0.796859	0.16327	0.0	4.66E-4	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507	T;T;T;T;T;T;T;T	0.43688	1.55;1.53;1.52;1.53;1.55;1.55;1.53;0.94	5.42	1.34	0.21922	.	0.317245	0.22025	N	0.065679	T	0.22044	0.0531	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.001;0.004;0.001;0.001;0.001	T	0.08126	-1.0737	10	0.31617	T	0.26	-3.1377	3.2049	0.06662	0.2076:0.1189:0.5513:0.1222	.	915;210;915;892;915	B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;KTN1_HUMAN	T	892;915;915;915;892;892;915;210	ENSP00000394992:A892T;ENSP00000378720:A915T;ENSP00000391964:A915T;ENSP00000378725:A915T;ENSP00000378719:A892T;ENSP00000378722:A892T;ENSP00000388807:A915T;ENSP00000452073:A210T	ENSP00000378719:A892T	A	+	1	0	KTN1	55189536	0.037000	0.19845	0.439000	0.26833	0.742000	0.42306	0.171000	0.16685	0.663000	0.31027	0.585000	0.79938	GCA	G|1.000;A|0.000	0.000	weak		0.274	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
AGGF1	55109	hgsc.bcm.edu	37	5	76331449	76331449	+	Missense_Mutation	SNP	G	G	A	rs34203073	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:76331449G>A	ENST00000312916.7	+	3	779	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	AGGF1_ENST00000506806.1_Missense_Mutation_p.E133K|AGGF1_ENST00000503538.1_3'UTR	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	133			E -> K (in KTS; in 5 patients; displays a stronger angiogenic activity; dbSNP:rs34203073). {ECO:0000269|PubMed:14961121}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TCAAGCTATCGAAACTTCTAT	0.328													G|||	39	0.00778754	0.0045	0.0058	5008	,	,		18392	0.001		0.0219	False		,,,				2504	0.0061				p.E133K		Atlas-SNP	.											AGGF1,colon,carcinoma,0,1	AGGF1	71	1	0			c.G397A	GRCh37	CM040277	AGGF1	M	rs34203073	scavenged	.	G	LYS/GLU	17,4389	24.3+/-50.5	0,17,2186	75.0	78.0	77.0		397	1.1	0.0	5	dbSNP_126	77	168,8430	77.2+/-139.8	2,164,4133	yes	missense	AGGF1	NM_018046.4	56	2,181,6319	AA,AG,GG		1.9539,0.3858,1.4226	benign	133/715	76331449	185,12819	2203	4299	6502	SO:0001583	missense	55109	exon3			GCTATCGAAACTT	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.397G>A	5.37:g.76331449G>A	ENSP00000316109:p.Glu133Lys	208.0	2.0	0.00961538		244.0	105.0	0.430328	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	19	0.0086996336996337	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	7.640	0.680759	0.14907	0.003858	0.019539	ENSG00000164252	ENST00000312916;ENST00000506806	T;T	0.79653	1.14;-1.29	5.96	1.13	0.20643	.	0.387612	0.28510	N	0.015088	T	0.49762	0.1576	L	0.43152	1.355	0.09310	N	1	B;B	0.13145	0.002;0.007	B;B	0.09377	0.001;0.004	T	0.40156	-0.9578	10	0.25106	T	0.35	-19.1001	2.2151	0.03957	0.2699:0.1226:0.4876:0.1198	rs34203073	133;133	Q8N302;Q8N302-3	AGGF1_HUMAN;.	K	133	ENSP00000316109:E133K;ENSP00000424733:E133K	ENSP00000316109:E133K	E	+	1	0	AGGF1	76367205	0.047000	0.20315	0.000000	0.03702	0.004000	0.04260	0.750000	0.26334	-0.075000	0.12798	-0.143000	0.13931	GAA	G|0.986;A|0.014	0.014	strong		0.328	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
EPG5	57724	hgsc.bcm.edu	37	18	43514856	43514856	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43514856G>A	ENST00000282041.5	-	11	2210	c.2176C>T	c.(2176-2178)Ctc>Ttc	p.L726F		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	726					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGGTGCATGAGGTAGAAGAGC	0.562																																					p.L726F		Atlas-SNP	.											.	EPG5	199	.	0			c.C2176T						PASS	.						65.0	66.0	66.0					18																	43514856		2017	4185	6202	SO:0001583	missense	57724	exon11			GCATGAGGTAGAA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.2176C>T	18.37:g.43514856G>A	ENSP00000282041:p.Leu726Phe	120.0	0.0	0		140.0	60.0	0.428571	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201595	0.58234	.	.	ENSG00000152223	ENST00000282041	T	0.12879	2.64	5.49	3.59	0.41128	.	0.761961	0.12243	N	0.486318	T	0.12305	0.0299	L	0.50333	1.59	0.36997	D	0.895098	B;B	0.13145	0.007;0.007	B;B	0.09377	0.004;0.004	T	0.08330	-1.0727	10	0.25751	T	0.34	-7.8907	6.4791	0.22053	0.0758:0.1864:0.6245:0.1132	.	726;726	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	F	726	ENSP00000282041:L726F	ENSP00000282041:L726F	L	-	1	0	EPG5	41768854	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.282000	0.43461	1.451000	0.47736	-0.150000	0.13652	CTC	.	.	none		0.562	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
MCCC1	56922	hgsc.bcm.edu	37	3	182804555	182804555	+	Missense_Mutation	SNP	C	C	T	rs375244642		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182804555C>T	ENST00000265594.4	-	4	441	c.295G>A	c.(295-297)Ggc>Agc	p.G99S	MCCC1_ENST00000492597.1_5'UTR|MCCC1_ENST00000539926.1_Intron	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	99	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	GGAGCGGGGCCGATGGAATAT	0.463																																					p.G99S		Atlas-SNP	.											.	MCCC1	87	.	0			c.G295A						PASS	.	C	SER/GLY	0,4406		0,0,2203	82.0	69.0	73.0		295	5.5	0.3	3		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	MCCC1	NM_020166.3	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	99/726	182804555	1,13005	2203	4300	6503	SO:0001583	missense	56922	exon4			CGGGGCCGATGGA	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.295G>A	3.37:g.182804555C>T	ENSP00000265594:p.Gly99Ser	80.0	0.0	0		60.0	28.0	0.466667	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.180502	0.78677	0.0	1.16E-4	ENSG00000078070	ENST00000265594;ENST00000476176;ENST00000448585	D;D	0.97811	-4.55;-4.55	5.5	5.5	0.81552	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99149	0.9706	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99289	1.0898	10	0.87932	D	0	.	18.991	0.92793	0.0:1.0:0.0:0.0	.	52;99	E9PG35;Q96RQ3	.;MCCA_HUMAN	S	99;52;52	ENSP00000265594:G99S;ENSP00000420433:G52S	ENSP00000265594:G99S	G	-	1	0	MCCC1	184287249	1.000000	0.71417	0.319000	0.25293	0.163000	0.22366	7.160000	0.77495	2.601000	0.87937	0.563000	0.77884	GGC	.	.	weak		0.463	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580963	140580963	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140580963C>T	ENST00000354757.3	+	1	1616	c.1616C>T	c.(1615-1617)cCg>cTg	p.P539L	PCDHB11_ENST00000536699.1_Missense_Mutation_p.P174L	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	539	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCGGCTCCCCGGCTTTGAGC	0.677																																					p.P539L		Atlas-SNP	.											.	PCDHB11	162	.	0			c.C1616T						PASS	.						35.0	48.0	44.0					5																	140580963		2202	4297	6499	SO:0001583	missense	56125	exon1			GCTCCCCGGCTTT	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1616C>T	5.37:g.140580963C>T	ENSP00000346802:p.Pro539Leu	203.0	0.0	0		150.0	59.0	0.393333	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	c	17.38	3.375882	0.61735	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01647	4.71;4.71	2.51	2.51	0.30379	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.09905	0.0243	M	0.80616	2.505	0.50467	D	0.999876	D	0.89917	1.0	D	0.97110	1.0	T	0.03354	-1.1045	9	0.87932	D	0	.	13.0572	0.58988	0.0:1.0:0.0:0.0	.	539	Q9Y5F2	PCDBB_HUMAN	L	174;539	ENSP00000440344:P174L;ENSP00000346802:P539L	ENSP00000346802:P539L	P	+	2	0	PCDHB11	140561147	0.996000	0.38824	0.014000	0.15608	0.076000	0.17211	3.578000	0.53892	1.412000	0.46977	0.298000	0.19748	CCG	.	.	none		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
OR2T1	26696	hgsc.bcm.edu	37	1	248570057	248570057	+	Silent	SNP	T	T	C	rs138375160	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248570057T>C	ENST00000366474.1	+	1	762	c.762T>C	c.(760-762)gtT>gtC	p.V254V		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTGCTGTGTTTTGATGCTGC	0.512													.|||	12	0.00239617	0.0	0.0014	5008	,	,		24031	0.0		0.0099	False		,,,				2504	0.001				p.V254V		Atlas-SNP	.											.	OR2T1	89	.	0			c.T762C						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	275.0	231.0	246.0		762	-9.5	0.0	1	dbSNP_134	246	80,8520	45.8+/-104.6	1,78,4221	no	coding-synonymous	OR2T1	NM_030904.1		1,88,6414	CC,CT,TT		0.9302,0.227,0.692		254/370	248570057	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	26696	exon1			CTGTGTTTTGATG	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.762T>C	1.37:g.248570057T>C		181.0	0.0	0		157.0	73.0	0.464968	NM_030904	Q6IEZ9	Silent	SNP	ENST00000366474.1	37	CCDS31115.1																																																																																			T|0.994;C|0.006	0.006	strong		0.512	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2		
ALB	213	hgsc.bcm.edu	37	4	74280774	74280774	+	Silent	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:74280774A>C	ENST00000503124.1	+	7	838	c.631A>C	c.(631-633)Agg>Cgg	p.R211R	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Silent_p.R246R|ALB_ENST00000415165.2_Silent_p.R169R|ALB_ENST00000509063.1_Silent_p.R361R|ALB_ENST00000295897.4_Silent_p.R361R			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATATGCAAGAAGGCATCCTGA	0.378																																					p.R361R		Atlas-SNP	.											.	ALB	132	.	0			c.A1081C						PASS	.						149.0	149.0	149.0					4																	74280774		2203	4300	6503	SO:0001819	synonymous_variant	213	exon9			GCAAGAAGGCATC	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.631A>C	4.37:g.74280774A>C		98.0	0.0	0		125.0	30.0	0.24	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	A	8.900	0.956161	0.18507	.	.	ENSG00000163631	ENST00000511370	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.71375	0.3332	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70502	-0.4854	4	.	.	.	-18.0923	15.0348	0.71738	1.0:0.0:0.0:0.0	.	.	.	.	T	205	.	.	K	+	2	0	ALB	74499638	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	4.402000	0.59722	2.232000	0.73038	0.533000	0.62120	AAG	.	.	none		0.378	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
SF3B1	23451	hgsc.bcm.edu	37	2	198270136	198270136	+	Missense_Mutation	SNP	T	T	C	rs367701030		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:198270136T>C	ENST00000335508.6	-	10	1391	c.1300A>G	c.(1300-1302)Act>Gct	p.T434A	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	434	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GGTGTTGGAGTAGCTGTCAGC	0.398			Mis		myelodysplastic syndrome																																p.T434A		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.A1300G						PASS	.						50.0	50.0	50.0					2																	198270136		2203	4300	6503	SO:0001583	missense	23451	exon10			TTGGAGTAGCTGT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1300A>G	2.37:g.198270136T>C	ENSP00000335321:p.Thr434Ala	177.0	0.0	0		156.0	44.0	0.282051	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.549172	0.65311	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.66	5.66	0.87406	Splicing factor 3B subunit 1 (1);	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.80746	2.51	0.80722	D	1	B	0.31752	0.338	B	0.38194	0.267	T	0.73597	-0.3932	9	0.45353	T	0.12	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	434	O75533	SF3B1_HUMAN	A	434	.	ENSP00000335321:T434A	T	-	1	0	SF3B1	197978381	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.883000	0.87264	2.280000	0.76307	0.533000	0.62120	ACT	.	.	alt		0.398	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909573	2909573	+	Missense_Mutation	SNP	G	G	A	rs139893801	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2909573G>A	ENST00000533594.1	-	4	1095	c.599C>T	c.(598-600)aCa>aTa	p.T200I	CDKN1C_ENST00000440480.2_5'Flank|SLC22A18AS_ENST00000526203.1_Missense_Mutation_p.T97I|CDKN1C_ENST00000313407.6_5'Flank|SLC22A18AS_ENST00000455942.2_Missense_Mutation_p.T97I|CDKN1C_ENST00000414822.3_5'Flank|CDKN1C_ENST00000430149.2_5'Flank|CDKN1C_ENST00000380725.1_5'Flank	NM_007105.2	NP_009036.2	Q8N1D0	BWR1B_HUMAN	solute carrier family 22 (organic cation transporter), member 18 antisense	200										NS(1)|endometrium(2)	3						TTCACGTCCTGTCATTCTTGC	0.577											OREG0020687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	5	0.000998403	0.0015	0.0029	5008	,	,		12996	0.0		0.001	False		,,,				2504	0.0				p.T200I		Atlas-SNP	.											.	SLC22A18AS	7	.	0			c.C599T						PASS	.						130.0	110.0	116.0					11																	2909573		692	1591	2283	SO:0001583	missense	5003	exon4			CGTCCTGTCATTC	AF035407	CCDS7739.1	11p15.5	2011-02-10	2005-08-23	2005-08-23	ENSG00000254827	ENSG00000254827			10965	protein-coding gene	gene with protein product		603240	"""solute carrier family 22 (organic cation transporter), member 1-like antisense"""	BWSCR1B, ORCTL2S, SLC22A1LS		9570947, 9520460, 15175115	Standard	NM_007105		Approved	BWR1B, p27-BWR1B	uc001lwv.4	Q8N1D0	OTTHUMG00000010038	ENST00000533594.1:c.599C>T	11.37:g.2909573G>A	ENSP00000433282:p.Thr200Ile	60.0	0.0	0	607	64.0	33.0	0.515625	NM_007105	E9PLK8|O43563	Missense_Mutation	SNP	ENST00000533594.1	37	CCDS7739.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	G	12.71	2.018667	0.35606	.	.	ENSG00000254827	ENST00000533594;ENST00000526203;ENST00000455942	T;T;T	0.53206	1.22;0.63;0.63	1.51	0.449	0.16619	.	.	.	.	.	T	0.33294	0.0858	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	P	0.51945	0.685	T	0.17107	-1.0380	9	0.87932	D	0	.	5.3284	0.15918	0.0:0.3666:0.6334:0.0	.	200	E9PLK8	.	I	200;97;97	ENSP00000433282:T200I;ENSP00000435592:T97I;ENSP00000434027:T97I	ENSP00000434027:T97I	T	-	2	0	SLC22A18AS	2866149	0.001000	0.12720	0.000000	0.03702	0.661000	0.39034	0.408000	0.21065	0.157000	0.19338	0.313000	0.20887	ACA	G|0.999;A|0.001	0.001	strong		0.577	SLC22A18AS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027771.3	NM_007105	
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68765205C>T	ENST00000303795.4	+	7	1177	c.1006C>T	c.(1006-1008)Ctt>Ttt	p.L336F	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	336			L -> F (in dbSNP:rs13404469).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGGCGACTCACTTCAGGATGA	0.423													T|||	395	0.0788738	0.1483	0.0735	5008	,	,		18007	0.005		0.0726	False		,,,				2504	0.0716				p.L336F		Atlas-SNP	.											.	APLF	69	.	0			c.C1006T						PASS	.	T	PHE/LEU	637,3769		51,535,1617	92.0	86.0	88.0		1006	4.0	0.0	2	dbSNP_121	88	695,7905		33,629,3638	yes	missense	APLF	NM_173545.2	22	84,1164,5255	TT,TC,CC		8.0814,14.4576,10.2414	benign	336/512	68765205	1332,11674	2203	4300	6503	SO:0001583	missense	200558	exon7			GACTCACTTCAGG	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1006C>T	2.37:g.68765205C>T	ENSP00000307004:p.Leu336Phe	173.0	0.0	0		123.0	91.0	0.739837	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	151	0.06913919413919414	62	0.12601626016260162	28	0.07734806629834254	4	0.006993006993006993	57	0.07519788918205805	.	0.181	-1.061812	0.01950	0.144576	0.080814	ENSG00000169621	ENST00000303795	T	0.23950	1.88	5.19	4.0	0.46444	.	1.310930	0.04804	N	0.434102	T	0.00073	0.0002	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.26408	T	0.33	.	8.0877	0.30782	0.0:0.1667:0.0:0.8333	rs13404469;rs52799369;rs13404469	336	Q8IW19	APLF_HUMAN	F	336	ENSP00000307004:L336F	ENSP00000307004:L336F	L	+	1	0	APLF	68618709	0.006000	0.16342	0.002000	0.10522	0.063000	0.16089	0.651000	0.24873	0.274000	0.22072	-0.381000	0.06696	CTT	C|0.910;T|0.090	0.090	strong		0.423	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
OR12D3	81797	hgsc.bcm.edu	37	6	29342271	29342271	+	Missense_Mutation	SNP	G	G	A	rs369042428		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29342271G>A	ENST00000396806.3	-	1	797	c.794C>T	c.(793-795)aCc>aTc	p.T265I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						AATCATGGAGGTGGCTGAAGC	0.473																																					p.T265I		Atlas-SNP	.											.	OR12D3	55	.	0			c.C794T						PASS	.	G	ILE/THR	0,3018		0,0,1509	91.0	84.0	86.0		794	1.0	0.0	6		86	1,5413		0,1,2706	no	missense	OR12D3	NM_030959.2	89	0,1,4215	AA,AG,GG		0.0185,0.0,0.0119	possibly-damaging	265/317	29342271	1,8431	1509	2707	4216	SO:0001583	missense	81797	exon1			ATGGAGGTGGCTG		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.794C>T	6.37:g.29342271G>A	ENSP00000380023:p.Thr265Ile	124.0	0.0	0		106.0	29.0	0.273585	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.263638	0.23136	0.0	1.85E-4	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.00107	8.72	4.19	1.0	0.19881	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.17674	0.51	0.09310	N	1	P	0.48834	0.916	P	0.51550	0.673	T	0.00809	-1.1557	9	0.33141	T	0.24	-7.0619	8.4505	0.32869	0.0:0.1285:0.4082:0.4634	.	265	Q9UGF7	O12D3_HUMAN	I	265	ENSP00000380023:T265I	ENSP00000366348:T265I	T	-	2	0	OR12D3	29450250	0.000000	0.05858	0.000000	0.03702	0.297000	0.27493	0.837000	0.27558	0.342000	0.23796	0.205000	0.17691	ACC	.	.	weak		0.473	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
EEF1D	1936	hgsc.bcm.edu	37	8	144671955	144671955	+	Intron	SNP	C	C	T	rs61757370	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144671955C>T	ENST00000529272.1	-	2	397				EEF1D_ENST00000442189.2_Silent_p.A99A|EEF1D_ENST00000423316.2_Silent_p.A99A|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000532741.1_Silent_p.A149A|EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000524624.1_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			GGGCCAGGTCCGCGGGGCCGA	0.662													C|||	63	0.0125799	0.0454	0.0043	5008	,	,		14599	0.0		0.0	False		,,,				2504	0.0				p.A99A		Atlas-SNP	.											.	EEF1D	48	.	0			c.G297A						PASS	.	C	,,,,,,	197,4199		3,191,2004	20.0	22.0	21.0		297,,,,,,297	-7.0	0.0	8	dbSNP_129	21	8,8590		0,8,4291	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	EEF1D	NM_001130053.2,NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1,NM_001960.4,NM_032378.4	,,,,,,	3,199,6295	TT,TC,CC		0.093,4.4813,1.5777	,,,,,,	99/648,,,,,,99/648	144671955	205,12789	2198	4299	6497	SO:0001627	intron_variant	1936	exon3			CAGGTCCGCGGGG	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.4-2936G>A	8.37:g.144671955C>T		53.0	0.0	0		55.0	29.0	0.527273	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																			C|0.987;T|0.013	0.013	strong		0.662	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378	
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28898778C>G	ENST00000357084.3	+	8	930	c.663C>G	c.(661-663)ggC>ggG	p.G221G	ATP2A1_ENST00000395503.4_Silent_p.G221G|ATP2A1_ENST00000536376.1_Silent_p.G96G	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	221					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGCCTTGGGCATCGTGGCCA	0.607													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18988	0.0		0.008	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C663G						PASS	.	C	,	7,4387	12.9+/-30.5	0,7,2190	85.0	82.0	83.0		663,663	3.4	1.0	16	dbSNP_132	83	72,8528	43.6+/-101.6	1,70,4229	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1,77,6419	GG,GC,CC		0.8372,0.1593,0.608	,	221/995,221/1002	28898778	79,12915	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CTTGGGCATCGTG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.663C>G	16.37:g.28898778C>G		65.0	0.0	0		69.0	39.0	0.565217	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			C|0.995;G|0.005	0.005	strong		0.607	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
DACT2	168002	hgsc.bcm.edu	37	6	168708678	168708678	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:168708678C>G	ENST00000366795.3	-	4	1847	c.1759G>C	c.(1759-1761)Gcc>Ccc	p.A587P	DACT2_ENST00000607983.1_Missense_Mutation_p.A179P|DACT2_ENST00000610183.1_Missense_Mutation_p.A417P|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	587					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		AGGGCTTGGGCTGAGGTCCGG	0.687																																					p.A587P		Atlas-SNP	.											.	DACT2	46	.	0			c.G1759C						PASS	.						27.0	35.0	33.0					6																	168708678		692	1591	2283	SO:0001583	missense	168002	exon4			CTTGGGCTGAGGT	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1759G>C	6.37:g.168708678C>G	ENSP00000355760:p.Ala587Pro	59.0	0.0	0		41.0	8.0	0.195122	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Missense_Mutation	SNP	ENST00000366795.3	37	CCDS47519.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.625905	0.28889	.	.	ENSG00000164488	ENST00000366795	T	0.48201	0.82	3.45	0.161	0.14977	.	0.724075	0.12669	N	0.448893	T	0.11793	0.0287	L	0.31752	0.955	0.09310	N	0.999991	P	0.38078	0.617	B	0.36289	0.221	T	0.13953	-1.0490	10	0.38643	T	0.18	-13.4784	2.1044	0.03688	0.2703:0.4574:0.1603:0.112	.	587	Q5SW24	DACT2_HUMAN	P	587	ENSP00000355760:A587P	ENSP00000355760:A587P	A	-	1	0	DACT2	168451527	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	0.037000	0.13840	-0.250000	0.09555	0.555000	0.69702	GCC	.	.	none		0.687	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28995211C>T	ENST00000311008.11	+	11	1802	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G	LAT_ENST00000454369.2_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000323081.8_Silent_p.G402G|LAT_ENST00000566177.1_5'Flank|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000352260.7_Silent_p.G401G|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000354453.4_5'Flank|SPNS1_ENST00000565975.1_Silent_p.G520G|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000395461.3_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	475					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACTGGGCGGCGCAGCCTTCC	0.672													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18700	0.0		0.008	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1425T						PASS	.	C	,,,,	7,4387	12.9+/-30.5	0,7,2190	48.0	51.0	50.0		1425,1203,1206,1269,1425	-9.2	0.1	16	dbSNP_132	50	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	1,79,6417	TT,TC,CC		0.8605,0.1593,0.6234	,,,,	475/529,401/455,402/456,423/477,475/529	28995211	81,12913	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			GGGCGGCGCAGCC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1425C>T	16.37:g.28995211C>T		44.0	0.0	0		44.0	24.0	0.545455	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.995;T|0.005	0.005	strong		0.672	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
TREX2	11219	hgsc.bcm.edu	37	X	152710522	152710522	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:152710522C>A	ENST00000334497.2	-	11	1637	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	TREX2_ENST00000338525.2_Missense_Mutation_p.D123Y|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000370231.2_Missense_Mutation_p.D123Y|TREX2_ENST00000330912.2_Missense_Mutation_p.D123Y|TREX2_ENST00000402951.1_Missense_Mutation_p.D166Y|TREX2_ENST00000370232.1_Missense_Mutation_p.D166Y|TREX2_ENST00000393862.2_Missense_Mutation_p.D123Y|TREX2_ENST00000414588.1_Missense_Mutation_p.D165Y			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	166					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGGGGAAATCATAATCAAAG	0.692								Editing and processing nucleases																													p.D123Y		Atlas-SNP	.											.	TREX2	36	.	0			c.G367T						PASS	.						7.0	6.0	7.0					X																	152710522		2093	4103	6196	SO:0001583	missense	11219	exon2			GGAAATCATAATC	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.496G>T	X.37:g.152710522C>A	ENSP00000334993:p.Asp166Tyr	21.0	0.0	0		20.0	7.0	0.35	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	C	18.63	3.664993	0.67700	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	D;D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.01	5.01	0.66863	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.50627	U	0.000120	D	0.92721	0.7686	M	0.85041	2.73	0.47374	D	0.999401	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93907	0.7193	10	0.87932	D	0	-19.851	14.7609	0.69604	0.0:1.0:0.0:0.0	.	165;166	Q06S70;Q9BQ50	.;TREX2_HUMAN	Y	123;123;123;166;166;166;165;123	ENSP00000377442:D123Y;ENSP00000333441:D123Y;ENSP00000345218:D123Y;ENSP00000334993:D166Y;ENSP00000359252:D166Y;ENSP00000386078:D166Y;ENSP00000401692:D165Y;ENSP00000359251:D123Y	ENSP00000333441:D123Y	D	-	1	0	TREX2	152363716	0.982000	0.34865	0.989000	0.46669	0.687000	0.40016	2.609000	0.46317	2.067000	0.61834	0.468000	0.43344	GAT	.	.	none		0.692	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701	
VWA3A	146177	hgsc.bcm.edu	37	16	22143031	22143031	+	Missense_Mutation	SNP	G	G	A	rs199942653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:22143031G>A	ENST00000389398.5	+	19	1949	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	618	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		TTCACTGGGGGCATCCCCGAC	0.567																																					p.G618D		Atlas-SNP	.											.	VWA3A	115	.	0			c.G1853A						PASS	.						52.0	56.0	55.0					16																	22143031		1951	4143	6094	SO:0001583	missense	146177	exon19			CTGGGGGCATCCC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.1853G>A	16.37:g.22143031G>A	ENSP00000374049:p.Gly618Asp	262.0	1.0	0.00381679		220.0	92.0	0.418182	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960192	0.74016	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.48836	0.8	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79155	-0.1920	10	0.87932	D	0	.	17.4177	0.87505	0.0:0.0:1.0:0.0	.	618;242	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	D	618;241	ENSP00000374049:G618D	ENSP00000299840:G241D	G	+	2	0	VWA3A	22050532	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	6.685000	0.74543	2.438000	0.82558	0.563000	0.77884	GGC	G|0.999;A|0.001	0.001	weak		0.567	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
USP11	8237	hgsc.bcm.edu	37	X	47092423	47092423	+	Missense_Mutation	SNP	G	G	A	rs149757747	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47092423G>A	ENST00000218348.3	+	1	110	c.110G>A	c.(109-111)tGt>tAt	p.C37Y	USP11_ENST00000377107.2_5'UTR	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	37					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						TGCGTTGGCTGTAGAAGAGAA	0.647																																					p.C37Y		Atlas-SNP	.											.	USP11	93	.	0			c.G110A						PASS	.	G	TYR/CYS	0,3835		0,0,0,1632,571	25.0	23.0	24.0		110	4.4	0.0	X	dbSNP_134	24	7,6721		0,4,3,2424,1869	yes	missense	USP11	NM_004651.3	194	0,4,3,4056,2440	AA,AG,A,GG,G		0.104,0.0,0.0663	possibly-damaging	37/964	47092423	7,10556	2203	4300	6503	SO:0001583	missense	8237	exon1			TTGGCTGTAGAAG	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.110G>A	X.37:g.47092423G>A	ENSP00000218348:p.Cys37Tyr	70.0	0.0	0		81.0	21.0	0.259259	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.984787	0.35036	0.0	0.00104	ENSG00000102226	ENST00000218348	T	0.21191	2.02	4.39	4.39	0.52855	.	.	.	.	.	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.15065	-1.0450	9	0.49607	T	0.09	2.5884	11.9698	0.53058	0.0:0.0:1.0:0.0	.	37	P51784	UBP11_HUMAN	Y	37	ENSP00000218348:C37Y	ENSP00000218348:C37Y	C	+	2	0	USP11	46977367	0.010000	0.17322	0.005000	0.12908	0.733000	0.41908	1.525000	0.35953	2.111000	0.64477	0.513000	0.50165	TGT	G|1.000;A|0.000	0.000	strong		0.647	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651	
LCMT2	9836	hgsc.bcm.edu	37	15	43621483	43621483	+	Missense_Mutation	SNP	C	C	T	rs144228208		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:43621483C>T	ENST00000305641.5	-	1	1320	c.1205G>A	c.(1204-1206)gGc>gAc	p.G402D	LCMT2_ENST00000544735.1_5'UTR|ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000567039.1_3'UTR|ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000389651.4_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	402					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	TATTTGGCTGCCTTTCCATTC	0.532																																					p.G402D		Atlas-SNP	.											LCMT2,NS,carcinoma,-1,1	LCMT2	48	1	0			c.G1205A						PASS	.	C	ASP/GLY	0,4402		0,0,2201	104.0	109.0	107.0		1205	3.0	1.0	15	dbSNP_134	107	4,8594	3.7+/-12.6	0,4,4295	yes	missense	LCMT2	NM_014793.4	94	0,4,6496	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging	402/687	43621483	4,12996	2201	4299	6500	SO:0001583	missense	9836	exon1			TGGCTGCCTTTCC	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 4"""	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.1205G>A	15.37:g.43621483C>T	ENSP00000307214:p.Gly402Asp	93.0	0.0	0		63.0	45.0	0.714286	NM_014793	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	37	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402603	0.25291	0.0	4.65E-4	ENSG00000168806	ENST00000305641	T	0.73897	-0.79	4.99	2.99	0.34606	.	0.852961	0.10614	N	0.654101	T	0.58977	0.2160	L	0.48362	1.52	0.80722	D	1	P	0.50272	0.933	B	0.36719	0.231	T	0.55854	-0.8075	10	0.13108	T	0.6	-26.0582	6.3112	0.21166	0.0:0.7148:0.1871:0.0981	.	402	O60294	LCMT2_HUMAN	D	402	ENSP00000307214:G402D	ENSP00000307214:G402D	G	-	2	0	LCMT2	41408775	0.204000	0.23447	0.985000	0.45067	0.712000	0.41017	1.513000	0.35823	1.479000	0.48272	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.532	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793	
DDX23	9416	hgsc.bcm.edu	37	12	49229991	49229991	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49229991A>G	ENST00000308025.3	-	11	1374	c.1295T>C	c.(1294-1296)aTt>aCt	p.I432T	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	432	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						AGCCACACCAATGATGTCACG	0.512																																					p.I432T		Atlas-SNP	.											.	DDX23	82	.	0			c.T1295C						PASS	.						198.0	183.0	188.0					12																	49229991		2203	4300	6503	SO:0001583	missense	9416	exon11			ACACCAATGATGT	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"""DEAD-boxes"""	17347	protein-coding gene	gene with protein product		612172	"""PRP28 homolog, yeast"""			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1295T>C	12.37:g.49229991A>G	ENSP00000310723:p.Ile432Thr	158.0	0.0	0		135.0	34.0	0.251852	NM_004818	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708132	0.89018	.	.	ENSG00000174243	ENST00000308025	T	0.16743	2.32	5.49	5.49	0.81192	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.44664	0.1304	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.48258	-0.9051	10	0.87932	D	0	-6.0539	14.5545	0.68091	1.0:0.0:0.0:0.0	.	432	Q9BUQ8	DDX23_HUMAN	T	432	ENSP00000310723:I432T	ENSP00000310723:I432T	I	-	2	0	DDX23	47516258	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.182000	0.94881	2.079000	0.62486	0.459000	0.35465	ATT	.	.	none		0.512	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842603	128842603	+	Silent	SNP	G	G	A	rs376118787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:128842603G>A	ENST00000310343.9	-	21	3755	c.3756C>T	c.(3754-3756)ccC>ccT	p.P1252P	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Silent_p.P903P|ARHGAP32_ENST00000392657.3_Silent_p.P903P	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1252					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TATTCTCTTCGGGGGACCCAG	0.483																																					p.P1252P		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C3756T						PASS	.	G	,	1,4401	2.1+/-5.4	0,1,2200	98.0	103.0	101.0		3756,2709	-3.5	0.9	11		101	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	1252/2088,903/1739	128842603	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon21			CTCTTCGGGGGAC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.3756C>T	11.37:g.128842603G>A		128.0	0.0	0		137.0	40.0	0.291971	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			.	.	weak		0.483	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
ABLIM3	22885	hgsc.bcm.edu	37	5	148618836	148618836	+	Missense_Mutation	SNP	C	C	T	rs201076202		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148618836C>T	ENST00000506113.1	+	11	1552	c.1070C>T	c.(1069-1071)tCc>tTc	p.S357F	RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000326685.7_Intron|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000519549.1_3'UTR|ABLIM3_ENST00000309868.7_Missense_Mutation_p.S357F|ABLIM3_ENST00000508983.1_Missense_Mutation_p.S357F|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000356541.3_Intron			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	357					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCCCTACTCCCAGGTAATT	0.488																																					p.S357F		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C1070T						PASS	.	C	PHE/SER	1,4405	2.1+/-5.4	0,1,2202	162.0	154.0	156.0		1070	5.0	1.0	5		156	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ABLIM3	NM_014945.2	155	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	357/684	148618836	3,13003	2203	4300	6503	SO:0001583	missense	22885	exon12			CCTACTCCCAGGT	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1070C>T	5.37:g.148618836C>T	ENSP00000425394:p.Ser357Phe	189.0	0.0	0		179.0	85.0	0.47486	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.896731	0.52121	2.27E-4	2.33E-4	ENSG00000173210	ENST00000309868;ENST00000506113;ENST00000508983	T;T;T	0.56103	0.54;0.54;0.48	5.01	5.01	0.66863	.	0.121045	0.56097	D	0.000022	T	0.39835	0.1093	L	0.28400	0.85	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23797	-1.0178	10	0.10377	T	0.69	.	16.4609	0.84044	0.0:1.0:0.0:0.0	.	357	O94929	ABLM3_HUMAN	F	357	ENSP00000310309:S357F;ENSP00000425394:S357F;ENSP00000420855:S357F	ENSP00000310309:S357F	S	+	2	0	ABLIM3	148599029	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	5.565000	0.67365	2.481000	0.83766	0.462000	0.41574	TCC	.	.	weak		0.488	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
BEST2	54831	hgsc.bcm.edu	37	19	12866544	12866544	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12866544C>T	ENST00000549706.1	+	7	1154	c.830C>T	c.(829-831)aCc>aTc	p.T277I	BEST2_ENST00000042931.1_Missense_Mutation_p.T277I|BEST2_ENST00000553030.1_Missense_Mutation_p.T277I			Q8NFU1	BEST2_HUMAN	bestrophin 2	277					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						CCCATCTTCACCCTCTTGCAG	0.577																																					p.T277I		Atlas-SNP	.											.	BEST2	35	.	0			c.C830T						PASS	.						105.0	107.0	106.0					19																	12866544		2064	4233	6297	SO:0001583	missense	54831	exon6			TCTTCACCCTCTT	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.830C>T	19.37:g.12866544C>T	ENSP00000448310:p.Thr277Ile	123.0	0.0	0		147.0	21.0	0.142857	NM_017682	Q53YQ8|Q9NXP0	Missense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547910	0.86022	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	D;D;D	0.99005	-5.32;-5.32;-5.32	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.99554	0.9840	H	0.97265	3.97	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	D	0.97764	1.0222	10	0.87932	D	0	-32.3086	16.2931	0.82759	0.0:1.0:0.0:0.0	.	277	Q8NFU1	BEST2_HUMAN	I	277	ENSP00000448310:T277I;ENSP00000447203:T277I;ENSP00000042931:T277I	ENSP00000042931:T277I	T	+	2	0	BEST2	12727544	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.507000	0.81676	2.362000	0.80069	0.650000	0.86243	ACC	.	.	none		0.577	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
DSG2	1829	hgsc.bcm.edu	37	18	29126108	29126108	+	Missense_Mutation	SNP	T	T	G	rs142841727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:29126108T>G	ENST00000261590.8	+	15	2968	c.2759T>G	c.(2758-2760)gTa>gGa	p.V920G	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	920			V -> G (in dbSNP:rs142841727). {ECO:0000269|PubMed:18678517, ECO:0000269|PubMed:19863551}.		apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			GCGCAAAAGGTAGCTACACCT	0.458													T|||	16	0.00319489	0.0	0.0101	5008	,	,		21083	0.0		0.0089	False		,,,				2504	0.0				p.V920G		Atlas-SNP	.											DSG2,NS,lymphoid_neoplasm,0,1	DSG2	115	1	0			c.T2759G	GRCh37	CM070920	DSG2	M	rs142841727	PASS	.	T	GLY/VAL	6,3890		0,6,1942	86.0	84.0	85.0		2759	2.5	0.0	18	dbSNP_134	85	41,8229		0,41,4094	yes	missense	DSG2	NM_001943.3	109	0,47,6036	GG,GT,TT		0.4958,0.154,0.3863	benign	920/1119	29126108	47,12119	1948	4135	6083	SO:0001583	missense	1829	exon15			AAAAGGTAGCTAC	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2759T>G	18.37:g.29126108T>G	ENSP00000261590:p.Val920Gly	116.0	0.0	0		107.0	53.0	0.495327	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	T	4.378	0.069751	0.08436	0.00154	0.004958	ENSG00000046604	ENST00000261590	T	0.77877	-1.13	4.9	2.5	0.30297	.	0.296289	0.24470	N	0.038257	T	0.53142	0.1778	L	0.36672	1.1	0.09310	N	0.999999	P	0.39282	0.666	B	0.32864	0.154	T	0.48714	-0.9011	10	0.38643	T	0.18	.	6.805	0.23772	0.0:0.29:0.0:0.71	.	920	Q14126	DSG2_HUMAN	G	920	ENSP00000261590:V920G	ENSP00000261590:V920G	V	+	2	0	DSG2	27380106	0.000000	0.05858	0.024000	0.17045	0.571000	0.35966	0.145000	0.16157	0.438000	0.26450	-0.250000	0.11733	GTA	T|0.995;G|0.005	0.005	strong		0.458	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
LOXHD1	125336	hgsc.bcm.edu	37	18	44159672	44159672	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44159672A>C	ENST00000398722.4	-	6	895	c.896T>G	c.(895-897)cTt>cGt	p.L299R	LOXHD1_ENST00000536736.1_Missense_Mutation_p.L577R|LOXHD1_ENST00000441551.2_Missense_Mutation_p.L577R			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	299	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						ATCACCAAAAAGGCAGAGATA	0.537																																					p.L577R		Atlas-SNP	.											.	LOXHD1	367	.	0			c.T1730G						PASS	.						287.0	259.0	268.0					18																	44159672		692	1591	2283	SO:0001583	missense	125336	exon13			CCAAAAAGGCAGA	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.896T>G	18.37:g.44159672A>C	ENSP00000381707:p.Leu299Arg	136.0	0.0	0		154.0	74.0	0.480519	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		.	.	.	.	.	.	.	.	.	.	A	14.68	2.606273	0.46527	.	.	ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730	T;T	0.74106	-0.81;-0.81	5.23	5.23	0.72850	.	0.278623	0.35615	N	0.003099	D	0.89791	0.6817	H	0.95679	3.705	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.974	D	0.92833	0.6282	10	0.87932	D	0	.	15.0711	0.72037	1.0:0.0:0.0:0.0	.	577;299	F5GZB4;Q8IVV2-2	.;.	R	299;577;299	ENSP00000381707:L299R;ENSP00000444586:L577R	ENSP00000338222:L299R	L	-	2	0	LOXHD1	42413670	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	8.153000	0.89640	2.099000	0.63709	0.379000	0.24179	CTT	.	.	none		0.537	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
MRC2	9902	hgsc.bcm.edu	37	17	60766283	60766283	+	Missense_Mutation	SNP	C	C	T	rs201851897		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:60766283C>T	ENST00000303375.5	+	23	3698	c.3296C>T	c.(3295-3297)aCg>aTg	p.T1099M	MRC2_ENST00000580916.1_3'UTR|MRC2_ENST00000446119.2_Missense_Mutation_p.R45W	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1099	C-type lectin 6. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CGGAGCTGCACGGAGGAGACC	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		19199	0.001		0.0	False		,,,				2504	0.0				p.T1099M		Atlas-SNP	.											MRC2,NS,carcinoma,0,1	MRC2	126	1	0			c.C3296T						PASS	.	C	MET/THR	0,4406		0,0,2203	46.0	39.0	42.0		3296	-1.2	0.0	17		42	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRC2	NM_006039.3	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1099/1480	60766283	1,13005	2203	4300	6503	SO:0001583	missense	9902	exon23			GCTGCACGGAGGA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3296C>T	17.37:g.60766283C>T	ENSP00000307513:p.Thr1099Met	135.0	0.0	0		118.0	35.0	0.29661	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	C|C	14.28|14.28	2.487814|2.487814	0.44249|0.44249	0.0|0.0	1.16E-4|1.16E-4	ENSG00000011028|ENSG00000011028	ENST00000446119|ENST00000303375	T|T	0.03301|0.20200	3.98|2.09	4.73|4.73	-1.2|-1.2	0.09554|0.09554	.|C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.|0.935369	.|0.09211	.|N	.|0.833271	T|T	0.21841|0.21841	0.0526|0.0526	M|M	0.75447|0.75447	2.3|2.3	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.17038	0.0|0.02	B|B	0.01281|0.12837	0.0|0.008	T|T	0.35649|0.35649	-0.9780|-0.9780	9|10	0.38643|0.51188	T|T	0.18|0.08	0.3399|0.3399	5.0404|5.0404	0.14456|0.14456	0.1411:0.3507:0.0:0.5082|0.1411:0.3507:0.0:0.5082	.|.	45|1099	E7EME3|Q9UBG0	.|MRC2_HUMAN	W|M	45|1099	ENSP00000400445:R45W|ENSP00000307513:T1099M	ENSP00000400445:R45W|ENSP00000307513:T1099M	R|T	+|+	1|2	2|0	MRC2|MRC2	58120015|58120015	0.003000|0.003000	0.15002|0.15002	0.023000|0.023000	0.16930|0.16930	0.918000|0.918000	0.54935|0.54935	0.763000|0.763000	0.26517|0.26517	-0.035000|-0.035000	0.13691|0.13691	0.561000|0.561000	0.74099|0.74099	CGG|ACG	C|1.000;T|0.000	0.000	strong		0.672	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
FOXO1	2308	hgsc.bcm.edu	37	13	41239736	41239736	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41239736C>T	ENST00000379561.5	-	1	998	c.614G>A	c.(613-615)aGc>aAc	p.S205N		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	205					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		GCCCGCCGAGCTGTTGCTGTC	0.657																																					p.S205N		Atlas-SNP	.											.	FOXO1	110	.	0			c.G614A						PASS	.						35.0	26.0	29.0					13																	41239736		2202	4299	6501	SO:0001583	missense	2308	exon1			GCCGAGCTGTTGC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.614G>A	13.37:g.41239736C>T	ENSP00000368880:p.Ser205Asn	106.0	0.0	0		207.0	46.0	0.222222	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	37	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.241699	0.79912	.	.	ENSG00000150907	ENST00000379561	D	0.94966	-3.57	3.93	3.93	0.45458	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.086726	0.85682	D	0.000000	D	0.96197	0.8760	L	0.56396	1.775	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.96779	0.9574	10	0.87932	D	0	-13.4585	14.9379	0.70970	0.0:1.0:0.0:0.0	.	205	Q12778	FOXO1_HUMAN	N	205	ENSP00000368880:S205N	ENSP00000368880:S205N	S	-	2	0	FOXO1	40137736	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.074000	0.76791	1.732000	0.51606	0.563000	0.77884	AGC	.	.	none		0.657	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
PYGL	5836	hgsc.bcm.edu	37	14	51378517	51378517	+	Missense_Mutation	SNP	C	C	G	rs35026927	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51378517C>G	ENST00000216392.7	-	16	2232	c.1900G>C	c.(1900-1902)Gac>Cac	p.D634H	RP11-218E20.5_ENST00000557343.1_RNA|PYGL_ENST00000532462.1_Missense_Mutation_p.D634H|PYGL_ENST00000544180.2_Missense_Mutation_p.D600H	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	634					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	ACCATAGGGTCATTGTTCACC	0.448													C|||	7	0.00139776	0.0	0.0072	5008	,	,		22205	0.0		0.002	False		,,,				2504	0.0				p.D634H		Atlas-SNP	.											PYGL,colon,carcinoma,+2,1	PYGL	77	1	0			c.G1900C						PASS	.	C	HIS/ASP,HIS/ASP	5,4401	9.9+/-24.2	0,5,2198	111.0	100.0	104.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1798,1900	5.6	1.0	14	dbSNP_126	104	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense	PYGL	NM_001163940.1,NM_002863.4	81,81	0,59,6444	GG,GC,CC		0.6279,0.1135,0.4536	probably-damaging,probably-damaging	600/814,634/848	51378517	59,12947	2203	4300	6503	SO:0001583	missense	5836	exon16			TAGGGTCATTGTT		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"""Glycogen phosphorylases"""	9725	protein-coding gene	gene with protein product	"""Hers disease"", ""glycogen storage disease type VI"", ""glycogen phosphorylase, liver form"""	613741	"""phosphorylase, glycogen; liver"""			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.1900G>C	14.37:g.51378517C>G	ENSP00000216392:p.Asp634His	160.0	0.0	0		164.0	81.0	0.493902	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	CCDS32080.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	26.3	4.720583	0.89205	0.001135	0.006279	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96365	-3.99;-3.99;-3.99	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.98670	0.9554	H	0.98996	4.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96269	0.9197	10	0.87932	D	0	-31.9632	18.6272	0.91344	0.0:1.0:0.0:0.0	rs35026927	600;600;634	F5H816;B4DUB7;P06737	.;.;PYGL_HUMAN	H	634;600;634	ENSP00000431657:D634H;ENSP00000443787:D600H;ENSP00000216392:D634H	ENSP00000216392:D634H	D	-	1	0	PYGL	50448267	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.792000	0.85828	2.646000	0.89796	0.467000	0.42956	GAC	C|0.996;G|0.004	0.004	strong		0.448	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
ACACB	32	hgsc.bcm.edu	37	12	109647006	109647006	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109647006C>T	ENST00000338432.7	+	21	3216	c.3097C>T	c.(3097-3099)Cgg>Tgg	p.R1033W	ACACB_ENST00000377854.5_Missense_Mutation_p.R1033W|ACACB_ENST00000377848.3_Missense_Mutation_p.R1033W			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1033					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GATGACCCTCCGGCACCCGTC	0.662																																					p.R1033W		Atlas-SNP	.											ACACB,caecum,adenoma,-1,1	ACACB	330	1	0			c.C3097T						PASS	.																																			SO:0001583	missense	32	exon20			ACCCTCCGGCACC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3097C>T	12.37:g.109647006C>T	ENSP00000341044:p.Arg1033Trp	109.0	0.0	0		115.0	51.0	0.443478	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325995	0.81580	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.50813	0.73;0.73;0.73	5.5	5.5	0.81552	Acetyl-CoA carboxylase, central domain (1);	0.056446	0.64402	D	0.000001	T	0.75243	0.3823	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.80125	-0.1513	10	0.87932	D	0	.	19.425	0.94737	0.0:1.0:0.0:0.0	.	1033	O00763	ACACB_HUMAN	W	1033;1033;1033;264	ENSP00000341044:R1033W;ENSP00000367079:R1033W;ENSP00000367085:R1033W	ENSP00000341044:R1033W	R	+	1	2	ACACB	108131389	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	4.052000	0.57420	2.584000	0.87258	0.563000	0.77884	CGG	.	.	none		0.662	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
EGFLAM	133584	hgsc.bcm.edu	37	5	38438505	38438505	+	Missense_Mutation	SNP	G	G	C	rs35767836	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:38438505G>C	ENST00000354891.3	+	17	2758	c.2412G>C	c.(2410-2412)gaG>gaC	p.E804D	EGFLAM_ENST00000397202.2_Missense_Mutation_p.E170D|EGFLAM_ENST00000322350.5_Missense_Mutation_p.E804D|EGFLAM_ENST00000336740.6_Missense_Mutation_p.E570D	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	804	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CCAGGAAGGAGGGCTATGACT	0.617													G|||	40	0.00798722	0.0015	0.0144	5008	,	,		14121	0.0		0.0239	False		,,,				2504	0.0041				p.E804D	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.G2412C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	23,4383	30.8+/-60.4	0,23,2180	39.0	39.0	39.0		2412,2412,1710	1.5	0.9	5	dbSNP_126	39	200,8400	86.6+/-149.0	4,192,4104	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	45,45,45	4,215,6284	CC,CG,GG		2.3256,0.522,1.7146	benign,benign,benign	804/1018,804/1010,570/776	38438505	223,12783	2203	4300	6503	SO:0001583	missense	133584	exon17			GAAGGAGGGCTAT	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2412G>C	5.37:g.38438505G>C	ENSP00000346964:p.Glu804Asp	107.0	0.0	0		123.0	54.0	0.439024	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	25	0.011446886446886446	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	19	0.025065963060686015	G	9.330	1.060369	0.19987	0.00522	0.023256	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580	T;T;T;D	0.92446	-1.19;-1.19;-1.19;-3.04	5.73	1.47	0.22746	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.143839	0.64402	N	0.000010	T	0.47210	0.1433	N	0.01209	-0.955	0.80722	D	1	B;B;B	0.12013	0.003;0.005;0.001	B;B;B	0.14023	0.008;0.01;0.008	T	0.52290	-0.8595	10	0.08837	T	0.75	-3.2598	3.303	0.06989	0.0786:0.2203:0.2607:0.4403	rs35767836	570;804;804	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	D	804;804;570;170;570	ENSP00000346964:E804D;ENSP00000313084:E804D;ENSP00000337607:E570D;ENSP00000380385:E170D	ENSP00000313084:E804D	E	+	3	2	EGFLAM	38474262	0.905000	0.30787	0.927000	0.36925	0.957000	0.61999	0.065000	0.14466	0.332000	0.23536	0.655000	0.94253	GAG	G|0.987;C|0.013	0.013	strong		0.617	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
NLRP8	126205	hgsc.bcm.edu	37	19	56473502	56473502	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56473502G>C	ENST00000291971.3	+	4	2183	c.2112G>C	c.(2110-2112)aaG>aaC	p.K704N	NLRP8_ENST00000590542.1_Missense_Mutation_p.K704N	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	704					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CGAATGATAAGCTGGAAGTCC	0.512																																					p.K704N		Atlas-SNP	.											.	NLRP8	225	.	0			c.G2112C						PASS	.						210.0	177.0	188.0					19																	56473502		2203	4300	6503	SO:0001583	missense	126205	exon4			TGATAAGCTGGAA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2112G>C	19.37:g.56473502G>C	ENSP00000291971:p.Lys704Asn	159.0	0.0	0		150.0	8.0	0.0533333	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.472569	0.00167	.	.	ENSG00000179709	ENST00000291971	D	0.88046	-2.33	1.93	-3.87	0.04218	.	.	.	.	.	T	0.54919	0.1888	N	0.00793	-1.18	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.54754	-0.8246	9	0.02654	T	1	.	5.0641	0.14572	0.0:0.4982:0.2851:0.2166	.	704;704	Q86W28-2;Q86W28	.;NALP8_HUMAN	N	704	ENSP00000291971:K704N	ENSP00000291971:K704N	K	+	3	2	NLRP8	61165314	0.002000	0.14202	0.000000	0.03702	0.010000	0.07245	-0.448000	0.06820	-1.456000	0.01921	-0.428000	0.05917	AAG	.	.	none		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
TIGD1	200765	hgsc.bcm.edu	37	2	233413648	233413648	+	Silent	SNP	G	G	A	rs72991949	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233413648G>A	ENST00000408957.3	-	1	1578	c.945C>T	c.(943-945)taC>taT	p.Y315Y	EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000258416.3_5'Flank|MIR5001_ENST00000580185.1_RNA|EIF4E2_ENST00000409322.1_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000409098.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409495.1_5'Flank	NM_145702.1	NP_663748.1	Q96MW7	TIGD1_HUMAN	tigger transposable element derived 1	315	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|skin(1)	2		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00842)|GBM - Glioblastoma multiforme(43;0.233)		taatctcctcgtatatctcca	0.403													G|||	760	0.151757	0.1051	0.134	5008	,	,		21198	0.1161		0.1938	False		,,,				2504	0.2209				p.Y315Y		Atlas-SNP	.											.	TIGD1	17	.	0			c.C945T						PASS	.	G		215,2183		7,201,991	3.0	3.0	3.0		945	0.5	1.0	2	dbSNP_130	3	569,3489		24,521,1484	no	coding-synonymous	TIGD1	NM_145702.1		31,722,2475	AA,AG,GG		14.0217,8.9658,12.1437		315/592	233413648	784,5672	1199	2029	3228	SO:0001819	synonymous_variant	200765	exon1			CTCCTCGTATATC		CCDS2495.1	2q37.1	2011-01-17			ENSG00000221944	ENSG00000221944			14523	protein-coding gene	gene with protein product		612972					Standard	NM_145702		Approved	EEYORE	uc002vsy.2	Q96MW7	OTTHUMG00000133260	ENST00000408957.3:c.945C>T	2.37:g.233413648G>A		4.0	0.0	0		4.0	4.0	1	NM_145702	Q6P4D2|Q6PIF9	Silent	SNP	ENST00000408957.3	37	CCDS2495.1																																																																																			G|0.858;A|0.142	0.142	strong		0.403	TIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257037.1	NM_145702	
SLITRK2	84631	hgsc.bcm.edu	37	X	144906370	144906370	+	Silent	SNP	A	A	G	rs45540333	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:144906370A>G	ENST00000370490.1	+	1	6682	c.2427A>G	c.(2425-2427)aaA>aaG	p.K809K	SLITRK2_ENST00000413937.2_Silent_p.K809K|SLITRK2_ENST00000434188.2_Silent_p.K809K|SLITRK2_ENST00000428560.2_Silent_p.K809K|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000447897.2_Silent_p.K809K			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	809					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CTCCCAGGAAATGCTTTGTGG	0.443													A|||	45	0.0119205	0.0008	0.0086	3775	,	,		14242	0.0		0.0209	False		,,,				2504	0.0174				p.K809K		Atlas-SNP	.											.	SLITRK2	221	.	0			c.A2427G						PASS	.	A	,,,,,,,	12,3823		0,11,1,1621,570	95.0	93.0	94.0		2427,2427,2427,2427,2427,2427,2427,2427	5.4	1.0	X	dbSNP_127	94	173,6555		1,120,51,2307,1821	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLITRK2	NM_001144003.2,NM_001144004.2,NM_001144005.2,NM_001144006.2,NM_001144008.2,NM_001144009.2,NM_001144010.2,NM_032539.4	,,,,,,,	1,131,52,3928,2391	GG,GA,G,AA,A		2.5713,0.3129,1.7514	,,,,,,,	809/846,809/846,809/846,809/846,809/846,809/846,809/846,809/846	144906370	185,10378	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CAGGAAATGCTTT	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2427A>G	X.37:g.144906370A>G		130.0	0.0	0		174.0	122.0	0.701149	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			A|0.986;G|0.014	0.014	strong		0.443	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
MYBL1	4603	hgsc.bcm.edu	37	8	67478431	67478431	+	Missense_Mutation	SNP	T	T	G	rs61729530	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67478431T>G	ENST00000522677.3	-	15	2408	c.1998A>C	c.(1996-1998)gaA>gaC	p.E666D	MYBL1_ENST00000522419.1_Intron|MYBL1_ENST00000517885.1_Missense_Mutation_p.E324D|MYBL1_ENST00000524176.2_Intron	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	666					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			TGTCATGTATTTCCAATAATG	0.279													T|||	27	0.00539137	0.0015	0.0058	5008	,	,		16344	0.002		0.0139	False		,,,				2504	0.0051				p.E666D		Atlas-SNP	.											.	MYBL1	73	.	0			c.A1998C						PASS	.	T	ASP/GLU,	16,3544		0,16,1764	130.0	107.0	114.0		1998,	4.7	1.0	8	dbSNP_129	114	118,7958		1,116,3921	yes	missense,intron	MYBL1	NM_001080416.2,NM_001144755.1	45,	1,132,5685	GG,GT,TT		1.4611,0.4494,1.1516	probably-damaging,	666/753,	67478431	134,11502	1780	4038	5818	SO:0001583	missense	4603	exon15			ATGTATTTCCAAT	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1998A>C	8.37:g.67478431T>G	ENSP00000429633:p.Glu666Asp	102.0	0.0	0		123.0	70.0	0.569106	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	18	0.008241758241758242	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	12	0.0158311345646438	T	18.91	3.724456	0.68959	0.004494	0.014611	ENSG00000185697	ENST00000522677;ENST00000517885	T;T	0.20069	2.58;2.1	5.87	4.73	0.59995	.	0.049569	0.85682	D	0.000000	T	0.24198	0.0586	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.04294	-1.0962	10	0.30078	T	0.28	-19.2094	8.646	0.34005	0.0:0.1422:0.0:0.8578	.	666	P10243	MYBA_HUMAN	D	666;324	ENSP00000429633:E666D;ENSP00000428265:E324D	ENSP00000428265:E324D	E	-	3	2	MYBL1	67640985	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.954000	0.49113	2.236000	0.73375	0.528000	0.53228	GAA	T|0.991;G|0.009	0.009	strong		0.279	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274	
FGD5	152273	hgsc.bcm.edu	37	3	14862049	14862049	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14862049G>A	ENST00000285046.5	+	1	1581	c.1471G>A	c.(1471-1473)Ggc>Agc	p.G491S	FGD5_ENST00000543601.1_Missense_Mutation_p.G250S	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	491					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GAAGGTGGCCGGCTATGTCCC	0.617																																					p.G491S		Atlas-SNP	.											FGD5_ENST00000285046,NS,carcinoma,0,2	FGD5	248	2	0			c.G1471A						PASS	.						39.0	43.0	42.0					3																	14862049		1938	4118	6056	SO:0001583	missense	152273	exon1			GTGGCCGGCTATG	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1471G>A	3.37:g.14862049G>A	ENSP00000285046:p.Gly491Ser	84.0	0.0	0		84.0	32.0	0.380952	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.532256	0.64972	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	D;D	0.89552	-2.53;-2.27	4.76	4.76	0.60689	.	0.000000	0.53938	D	0.000044	D	0.94202	0.8139	M	0.73598	2.24	0.47153	D	0.999332	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94924	0.8076	10	0.72032	D	0.01	-34.9884	17.8006	0.88586	0.0:0.0:1.0:0.0	.	250;491	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	S	491;250	ENSP00000285046:G491S;ENSP00000445949:G250S	ENSP00000285046:G491S	G	+	1	0	FGD5	14837053	1.000000	0.71417	0.525000	0.27900	0.087000	0.18053	5.876000	0.69667	2.206000	0.71126	0.585000	0.79938	GGC	.	.	none		0.617	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
LYST	1130	hgsc.bcm.edu	37	1	235887393	235887393	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235887393C>T	ENST00000389794.3	-	39	9424	c.9250G>A	c.(9250-9252)Gat>Aat	p.D3084N	LYST_ENST00000389793.2_Missense_Mutation_p.D3084N|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3084					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ACAGCATTATCTCTCAATTGC	0.363																																					p.D3084N		Atlas-SNP	.											.	LYST	370	.	0			c.G9250A						PASS	.						113.0	111.0	112.0					1																	235887393		2203	4300	6503	SO:0001583	missense	1130	exon39			CATTATCTCTCAA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9250G>A	1.37:g.235887393C>T	ENSP00000374444:p.Asp3084Asn	150.0	0.0	0		128.0	14.0	0.109375	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	34	5.344370	0.95807	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61980	0.06;0.06	5.23	5.23	0.72850	PH-BEACH domain (1);	0.046332	0.85682	N	0.000000	T	0.74145	0.3678	L	0.43646	1.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73104	-0.4088	10	0.44086	T	0.13	.	19.1565	0.93511	0.0:1.0:0.0:0.0	.	3084	Q99698	LYST_HUMAN	N	3084	ENSP00000374444:D3084N;ENSP00000374443:D3084N	ENSP00000374443:D3084N	D	-	1	0	LYST	233954016	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.776000	0.85560	2.597000	0.87782	0.460000	0.39030	GAT	.	.	none		0.363	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
HCAR1	27198	hgsc.bcm.edu	37	12	123214166	123214166	+	Missense_Mutation	SNP	G	G	A	rs140482291	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:123214166G>A	ENST00000436083.2	-	1	1224	c.721C>T	c.(721-723)Ctc>Ttc	p.L241F	HCAR1_ENST00000356987.2_Missense_Mutation_p.L241F|HCAR1_ENST00000432564.1_Missense_Mutation_p.L241F			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	241					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						AGGAAATAGAGTCTAGCAGAC	0.572													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18469	0.0		0.002	False		,,,				2504	0.0072				p.L241F		Atlas-SNP	.											.	HCAR1	21	.	0			c.C721T						PASS	.	G	PHE/LEU	0,4406		0,0,2203	69.0	64.0	66.0		721	4.6	0.1	12	dbSNP_134	66	13,8587	10.5+/-38.8	0,13,4287	yes	missense	HCAR1	NM_032554.3	22	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	probably-damaging	241/347	123214166	13,12993	2203	4300	6503	SO:0001583	missense	27198	exon1			AATAGAGTCTAGC	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	4532	protein-coding gene	gene with protein product	"""lactate receptor 1"""	606923	"""G protein-coupled receptor 104"", ""G protein-coupled receptor 81"""	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.721C>T	12.37:g.123214166G>A	ENSP00000409980:p.Leu241Phe	48.0	0.0	0		70.0	36.0	0.514286	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.74	2.327855	0.41197	0.0	0.001512	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.41758	0.99;0.99;0.99	5.51	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.295265	0.24568	N	0.037419	T	0.60366	0.2263	M	0.73372	2.23	0.09310	N	0.999998	D	0.71674	0.998	D	0.74348	0.983	T	0.54248	-0.8322	10	0.66056	D	0.02	-9.9997	10.1712	0.42911	0.0918:0.0:0.9082:0.0	.	241	Q9BXC0	HCAR1_HUMAN	F	241	ENSP00000349478:L241F;ENSP00000389255:L241F;ENSP00000409980:L241F	ENSP00000349478:L241F	L	-	1	0	HCAR1	121780119	0.181000	0.23161	0.126000	0.21872	0.428000	0.31595	1.981000	0.40628	1.326000	0.45319	0.655000	0.94253	CTC	G|0.998;A|0.002	0.002	strong		0.572	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1		
OR5K3	403277	hgsc.bcm.edu	37	3	98110414	98110414	+	Missense_Mutation	SNP	T	T	A	rs199575537		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:98110414T>A	ENST00000383695.1	+	1	905	c.905T>A	c.(904-906)aTt>aAt	p.I302N	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						ATGAAAAAAATTATGAAGAAG	0.264																																					p.I302N		Atlas-SNP	.											OR5K3,NS,carcinoma,0,2	OR5K3	60	2	0			c.T905A						scavenged	.						28.0	31.0	30.0					3																	98110414		2102	4200	6302	SO:0001583	missense	403277	exon1			AAAAAATTATGAA		CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.905T>A	3.37:g.98110414T>A	ENSP00000373194:p.Ile302Asn	23.0	0.0	0		27.0	2.0	0.0740741	NM_001005516		Missense_Mutation	SNP	ENST00000383695.1	37	CCDS33803.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.604568	0.28623	.	.	ENSG00000206536	ENST00000383695	T	0.39592	1.07	4.88	-2.06	0.07298	.	2.020920	0.02943	N	0.140719	T	0.35682	0.0940	L	0.52126	1.63	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.32693	-0.9897	10	0.66056	D	0.02	-0.152	3.649	0.08196	0.2583:0.2504:0.0:0.4913	.	302	A6NET4	OR5K3_HUMAN	N	302	ENSP00000373194:I302N	ENSP00000373194:I302N	I	+	2	0	OR5K3	99593104	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.590000	0.05760	-0.275000	0.09219	-0.416000	0.06073	ATT	.	.	weak		0.264	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1		
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55229255G>A	ENST00000275493.2	+	13	1739	c.1562G>A	c.(1561-1563)aGg>aAg	p.R521K	EGFR_ENST00000454757.2_Missense_Mutation_p.R468K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000344576.2_Missense_Mutation_p.R521K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	521			R -> K (in dbSNP:rs2227983). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.7}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCGGAGCCCAGGGACTGCGTC	0.617		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1463	0.292133	0.0643	0.33	5008	,	,		17432	0.5238		0.2763	False		,,,				2504	0.3507				p.R521K		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.G1562A	GRCh37	CM942312	EGFR	M	rs2227983	PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	391,4015	196.0+/-220.5	12,367,1824	111.0	114.0	113.0		1562,1562,1562	-5.8	0.0	7	dbSNP_98	113	2245,6355	380.6+/-339.7	317,1611,2372	yes	missense,missense,missense	EGFR	NM_005228.3,NM_201282.1,NM_201284.1	26,26,26	329,1978,4196	AA,AG,GG		26.1047,8.8743,20.2676	benign,benign,benign	521/1211,521/629,521/706	55229255	2636,10370	2203	4300	6503	SO:0001583	missense	1956	exon13	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AGCCCAGGGACTG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1562G>A	7.37:g.55229255G>A	ENSP00000275493:p.Arg521Lys	52.0	0.0	0		44.0	25.0	0.568182	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	652	0.29853479853479853	29	0.05894308943089431	108	0.2983425414364641	302	0.527972027972028	213	0.28100263852242746	G	1.353	-0.590998	0.03799	0.088743	0.261047	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	6.07	-5.79	0.02354	Growth factor, receptor (1);	1.067450	0.06989	N	0.821201	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.48043	-0.9069	9	0.10377	T	0.69	.	2.4933	0.04615	0.5094:0.1722:0.17:0.1484	rs2227983;rs3752650;rs11543848;rs12234746;rs17336807;rs11543848	476;521;521;521	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	K	476;521;391;521;521;521;468;315	ENSP00000415559:R476K;ENSP00000342376:R521K;ENSP00000345973:R521K;ENSP00000275493:R521K;ENSP00000410031:R521K;ENSP00000395243:R468K	ENSP00000275493:R521K	R	+	2	0	EGFR	55196749	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.793000	0.04589	-1.106000	0.03008	-0.165000	0.13383	AGG	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong		0.617	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
PCDH10	57575	hgsc.bcm.edu	37	4	134072208	134072208	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:134072208C>G	ENST00000264360.5	+	1	1739	c.913C>G	c.(913-915)Ccg>Gcg	p.P305A	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	305	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		CGGACTCTCGCCGCGCACTGG	0.637																																					p.P305A		Atlas-SNP	.											PCDH10,NS,carcinoma,-2,2	PCDH10	290	2	0			c.C913G						PASS	.						46.0	47.0	47.0					4																	134072208		2203	4300	6503	SO:0001583	missense	57575	exon1			CTCTCGCCGCGCA	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"""Cadherins / Protocadherins : Non-clustered"""	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.913C>G	4.37:g.134072208C>G	ENSP00000264360:p.Pro305Ala	58.0	0.0	0		43.0	10.0	0.232558	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320381	0.23994	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.53423	0.62	4.2	4.2	0.49525	Cadherin (4);Cadherin-like (1);	0.000000	0.44902	D	0.000415	T	0.43366	0.1244	L	0.46741	1.465	0.46260	D	0.998954	B;B	0.12013	0.002;0.005	B;B	0.17979	0.003;0.02	T	0.36672	-0.9738	10	0.37606	T	0.19	.	16.3343	0.83052	0.0:1.0:0.0:0.0	.	305;305	Q9P2E7;Q96SF0	PCD10_HUMAN;.	A	305	ENSP00000264360:P305A	ENSP00000264360:P305A	P	+	1	0	PCDH10	134291658	0.889000	0.30405	0.998000	0.56505	0.974000	0.67602	1.861000	0.39438	2.137000	0.66172	0.407000	0.27541	CCG	.	.	none		0.637	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570737	570737	+	Silent	SNP	G	G	A	rs142673366	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:570737G>A	ENST00000262305.4	+	14	2557	c.2169G>A	c.(2167-2169)gcG>gcA	p.A723A	RAB11FIP3_ENST00000450428.1_Silent_p.A427A|RAB11FIP3_ENST00000457159.1_Silent_p.A768A	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	723	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.				cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				TCATGGAGGCGATTCAGAAGC	0.582													G|||	3	0.000599042	0.0	0.0	5008	,	,		22162	0.0		0.003	False		,,,				2504	0.0				p.A723A	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.G2169A						PASS	.	G	,	1,4401	2.1+/-5.4	0,1,2200	128.0	104.0	112.0		1281,2169	-8.7	0.0	16	dbSNP_134	112	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	RAB11FIP3	NM_001142272.1,NM_014700.3	,	0,15,6486	AA,AG,GG		0.1628,0.0227,0.1154	,	427/461,723/757	570737	15,12987	2201	4300	6501	SO:0001819	synonymous_variant	9727	exon14			GGAGGCGATTCAG	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.2169G>A	16.37:g.570737G>A		91.0	0.0	0		93.0	37.0	0.397849	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700	
MBOAT1	154141	hgsc.bcm.edu	37	6	20124710	20124710	+	Missense_Mutation	SNP	G	G	A	rs146228602		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:20124710G>A	ENST00000324607.7	-	8	1000	c.836C>T	c.(835-837)cCg>cTg	p.P279L	MBOAT1_ENST00000541730.1_Missense_Mutation_p.P130L	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	279					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			GAGTCGAGCCGGAAAGCTTGC	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		24093	0.0		0.001	False		,,,				2504	0.0				p.P279L		Atlas-SNP	.											MBOAT1,NS,carcinoma,+1,1	MBOAT1	48	1	0			c.C836T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	162.0	140.0	147.0		836	0.6	0.4	6	dbSNP_134	147	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MBOAT1	NM_001080480.1	98	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	benign	279/496	20124710	11,12995	2203	4300	6503	SO:0001583	missense	154141	exon8			CGAGCCGGAAAGC	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.836C>T	6.37:g.20124710G>A	ENSP00000324944:p.Pro279Leu	92.0	0.0	0		85.0	14.0	0.164706	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	G	1.658	-0.512287	0.04200	0.0	0.001279	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.23950	1.88;1.88	5.61	0.549	0.17213	.	0.225123	0.38381	N	0.001710	T	0.01976	0.0062	N	0.02120	-0.675	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.48055	-0.9068	10	0.02654	T	1	-14.5864	9.466	0.38813	0.7298:0.0:0.2702:0.0	.	130;279	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	L	130;279	ENSP00000441568:P130L;ENSP00000324944:P279L	ENSP00000324944:P279L	P	-	2	0	MBOAT1	20232689	0.973000	0.33851	0.426000	0.26672	0.068000	0.16541	2.103000	0.41806	-0.061000	0.13110	-0.302000	0.09304	CCG	G|0.999;A|0.001	0.001	strong		0.448	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
HLTF	6596	hgsc.bcm.edu	37	3	148756993	148756993	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:148756993C>T	ENST00000310053.5	-	23	2832	c.2639G>A	c.(2638-2640)cGt>cAt	p.R880H	HLTF_ENST00000465259.1_Missense_Mutation_p.R879H|HLTF_ENST00000392912.2_Missense_Mutation_p.R880H|HLTF_ENST00000494055.1_Missense_Mutation_p.R880H	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	880	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			ACCATCCAAACGAGTAAACAC	0.343																																					p.R880H		Atlas-SNP	.											.	HLTF	87	.	0			c.G2639A						PASS	.						51.0	51.0	51.0					3																	148756993		2203	4300	6503	SO:0001583	missense	6596	exon23			TCCAAACGAGTAA	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.2639G>A	3.37:g.148756993C>T	ENSP00000308944:p.Arg880His	69.0	0.0	0		73.0	22.0	0.30137	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872131	0.91587	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000467858	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	5.98	5.98	0.97165	Helicase, C-terminal (3);	.	.	.	.	D	0.90820	0.7117	M	0.94021	3.485	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.92423	0.5947	9	0.87932	D	0	-17.5805	14.5887	0.68347	0.0:0.929:0.0:0.071	.	880;880;880	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	H	879;880;880;880;348	ENSP00000420745:R879H;ENSP00000308944:R880H;ENSP00000376644:R880H;ENSP00000420429:R880H;ENSP00000420106:R348H	ENSP00000308944:R880H	R	-	2	0	HLTF	150239683	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.529000	0.67135	2.835000	0.97688	0.650000	0.86243	CGT	.	.	none		0.343	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
OFD1	8481	hgsc.bcm.edu	37	X	13786875	13786875	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:13786875C>T	ENST00000340096.6	+	22	3294	c.2967C>T	c.(2965-2967)gaC>gaT	p.D989D	OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380567.1_Silent_p.D849D|OFD1_ENST00000380550.3_Silent_p.D949D	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	989	Mediates the interaction with SDCCAG8.				axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CCCTAGTGGACACGCTGCAAT	0.378																																					p.D989D		Atlas-SNP	.											.	OFD1	109	.	0			c.C2967T						PASS	.						155.0	148.0	150.0					X																	13786875		2203	4300	6503	SO:0001819	synonymous_variant	8481	exon22			AGTGGACACGCTG	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.2967C>T	X.37:g.13786875C>T		157.0	0.0	0		211.0	48.0	0.227488	NM_003611	B9ZVU5|O75666|Q4VAK4	Silent	SNP	ENST00000340096.6	37	CCDS14157.1																																																																																			.	.	none		0.378	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611	
MUC4	4585	hgsc.bcm.edu	37	3	195507998	195507998	+	Missense_Mutation	SNP	G	G	C	rs199622660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195507998G>C	ENST00000463781.3	-	2	10912	c.10453C>G	c.(10453-10455)Cac>Gac	p.H3485D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3485D|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGTAGAT	0.592																																					p.H3485D		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10453G						PASS	.						27.0	24.0	25.0					3																	195507998		671	1575	2246	SO:0001583	missense	4585	exon2			TGGTGTGACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10453C>G	3.37:g.195507998G>C	ENSP00000417498:p.His3485Asp	93.0	0.0	0		86.0	21.0	0.244186	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.390574	0.01185	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.56;1.54	0.743	-1.49	0.08718	.	.	.	.	.	T	0.21801	0.0525	N	0.08118	0	0.09310	N	1	P	0.50943	0.94	P	0.57502	0.822	T	0.12734	-1.0536	8	.	.	.	.	3.3352	0.07098	0.2419:0.273:0.4851:0.0	.	3357	E7ESK3	.	D	3485	ENSP00000417498:H3485D;ENSP00000420243:H3485D	.	H	-	1	0	MUC4	196992777	0.000000	0.05858	0.012000	0.15200	0.012000	0.07955	-0.405000	0.07196	-1.899000	0.01098	-1.880000	0.00545	CAC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
INO80D	54891	hgsc.bcm.edu	37	2	206872126	206872126	+	Silent	SNP	C	C	T	rs116331438	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:206872126C>T	ENST00000403263.1	-	10	2204	c.1800G>A	c.(1798-1800)ccG>ccA	p.P600P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P600P(1)|p.P495P(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CAATGTCATCCGGCAACTCAT	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.001				p.P600P		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	2	Substitution - coding silent(2)	kidney(2)	c.G1800A						PASS	.	C		3,4115		0,3,2056	130.0	130.0	130.0		1800	2.8	1.0	2	dbSNP_132	130	22,8406		0,22,4192	no	coding-synonymous	INO80D	NM_017759.4		0,25,6248	TT,TC,CC		0.261,0.0729,0.1993		600/1028	206872126	25,12521	2059	4214	6273	SO:0001819	synonymous_variant	54891	exon10			GTCATCCGGCAAC		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1800G>A	2.37:g.206872126C>T		202.0	0.0	0		241.0	118.0	0.489627	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
PCDHGA5	56110	hgsc.bcm.edu	37	5	140745959	140745959	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140745959G>A	ENST00000518069.1	+	1	2062	c.2062G>A	c.(2062-2064)Gac>Aac	p.D688N	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	688					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGGATCTGGACCTCACACT	0.597																																					p.D688N		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.G2062A						PASS	.						286.0	302.0	297.0					5																	140745959		2203	4299	6502	SO:0001583	missense	56110	exon1			GATCTGGACCTCA	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.2062G>A	5.37:g.140745959G>A	ENSP00000429834:p.Asp688Asn	128.0	0.0	0		101.0	48.0	0.475248	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	9.353	1.066093	0.20067	.	.	ENSG00000253485	ENST00000518069	T	0.50001	0.76	4.84	-0.0131	0.13985	.	.	.	.	.	T	0.37652	0.1011	L	0.45422	1.42	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.20384	0.029;0.02	T	0.31138	-0.9954	9	0.25106	T	0.35	.	10.8617	0.46831	0.2605:0.0:0.7395:0.0	.	688;688	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	N	688	ENSP00000429834:D688N	ENSP00000429834:D688N	D	+	1	0	PCDHGA5	140726143	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.324000	0.19610	0.125000	0.18397	0.563000	0.77884	GAC	.	.	none		0.597	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918	
LYST	1130	hgsc.bcm.edu	37	1	235918870	235918870	+	Silent	SNP	T	T	G	rs61738992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235918870T>G	ENST00000389794.3	-	25	7311	c.7137A>C	c.(7135-7137)ctA>ctC	p.L2379L	LYST_ENST00000389793.2_Silent_p.L2379L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2379					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ACTGGTTGGCTAGCAAGGAAA	0.343													T|||	105	0.0209665	0.0015	0.085	5008	,	,		16726	0.0		0.0298	False		,,,				2504	0.0143				p.L2379L		Atlas-SNP	.											.	LYST	370	.	0			c.A7137C						PASS	.	T		31,4375	37.6+/-69.7	0,31,2172	174.0	176.0	176.0		7137	-1.4	1.0	1	dbSNP_129	176	295,8305	107.4+/-168.2	3,289,4008	no	coding-synonymous	LYST	NM_000081.2		3,320,6180	GG,GT,TT		3.4302,0.7036,2.5065		2379/3802	235918870	326,12680	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon25			GTTGGCTAGCAAG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.7137A>C	1.37:g.235918870T>G		96.0	0.0	0		88.0	41.0	0.465909	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			T|0.976;G|0.024	0.024	strong		0.343	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
ARHGAP12	94134	hgsc.bcm.edu	37	10	32097650	32097650	+	Missense_Mutation	SNP	C	C	T	rs34750454		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:32097650C>T	ENST00000344936.2	-	19	2527	c.2293G>A	c.(2293-2295)Gtt>Att	p.V765I	ARHGAP12_ENST00000396144.4_Missense_Mutation_p.V760I|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.V735I|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.V713I|ARHGAP12_ENST00000492028.1_5'UTR|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.V713I	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	765	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				AGGTCCTTAACAGCAGCGACT	0.423																																					p.V765I		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.G2293A						PASS	.						301.0	261.0	274.0					10																	32097650		2203	4300	6503	SO:0001583	missense	94134	exon19			CCTTAACAGCAGC	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.2293G>A	10.37:g.32097650C>T	ENSP00000345808:p.Val765Ile	102.0	0.0	0		102.0	31.0	0.303922	NM_018287	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.961807	0.34659	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2	5.36	5.36	0.76844	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.119448	0.56097	D	0.000029	T	0.11836	0.0288	N	0.04275	-0.24	0.42256	D	0.991994	B;B;B;B;B;B	0.09022	0.001;0.002;0.002;0.002;0.002;0.0	B;B;B;B;B;B	0.29077	0.088;0.059;0.098;0.098;0.059;0.007	T	0.23154	-1.0196	10	0.26408	T	0.33	.	12.7667	0.57396	0.0:0.9245:0.0:0.0755	rs34750454	718;735;760;765;713;64	Q1RLN5;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3;Q9NV28	.;.;.;RHG12_HUMAN;.;.	I	713;735;765;760;713	ENSP00000310984:V713I;ENSP00000364399:V735I;ENSP00000345808:V765I;ENSP00000379448:V760I;ENSP00000364394:V713I	ENSP00000310984:V713I	V	-	1	0	ARHGAP12	32137656	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.129000	0.50500	2.667000	0.90743	0.650000	0.86243	GTT	C|0.987;T|0.013	0.013	weak		0.423	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
SEC61A1	29927	hgsc.bcm.edu	37	3	127774411	127774411	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:127774411T>C	ENST00000243253.3	+	3	312	c.128T>C	c.(127-129)tTa>tCa	p.L43S	SEC61A1_ENST00000464451.1_Missense_Mutation_p.L49S|SEC61A1_ENST00000424880.2_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	43					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)			central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						TTTATCTTCTTAGTGTGCTGC	0.458																																					p.L43S		Atlas-SNP	.											.	SEC61A1	39	.	0			c.T128C						PASS	.						185.0	176.0	179.0					3																	127774411		2203	4300	6503	SO:0001583	missense	29927	exon3			TCTTCTTAGTGTG	AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.128T>C	3.37:g.127774411T>C	ENSP00000243253:p.Leu43Ser	155.0	0.0	0		158.0	64.0	0.405063	NM_013336	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	37	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.777511	0.90195	.	.	ENSG00000058262	ENST00000464451;ENST00000243253	.	.	.	5.69	5.69	0.88448	Translocon Sec61/SecY, plug domain (1);SecY subunit domain (2);	0.000000	0.85682	D	0.000000	D	0.83788	0.5330	M	0.86573	2.825	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	D	0.86848	0.2021	9	0.87932	D	0	.	15.9604	0.79926	0.0:0.0:0.0:1.0	.	43	P61619	S61A1_HUMAN	S	49;43	.	ENSP00000243253:L43S	L	+	2	0	SEC61A1	129257101	1.000000	0.71417	0.993000	0.49108	0.883000	0.51084	8.035000	0.88872	2.168000	0.68352	0.528000	0.53228	TTA	.	.	none		0.458	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336	
AFAP1L1	134265	hgsc.bcm.edu	37	5	148695859	148695859	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148695859C>T	ENST00000296721.4	+	11	1358	c.1260C>T	c.(1258-1260)ccC>ccT	p.P420P	AFAP1L1_ENST00000515000.1_Silent_p.P420P	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	420	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGGTTCCCTGCTGTGGTG	0.647																																					p.P420P		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.C1260T						PASS	.						57.0	59.0	58.0					5																	148695859		2203	4300	6503	SO:0001819	synonymous_variant	134265	exon11			GGTTCCCTGCTGT	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.1260C>T	5.37:g.148695859C>T		91.0	0.0	0		124.0	13.0	0.104839	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	37	CCDS34274.1																																																																																			.	.	none		0.647	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406	
CXorf30	645090	hgsc.bcm.edu	37	X	36317108	36317108	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:36317108A>C	ENST00000378657.4	+	6	689	c.41A>C	c.(40-42)gAa>gCa	p.E14A		NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	14										breast(1)|lung(2)|stomach(1)	4						ACTTGCATTGAAATACCTCTC	0.358																																					p.E14A		Atlas-SNP	.											.	CXorf30	76	.	0			c.A41C						PASS	.						133.0	107.0	115.0					X																	36317108		692	1591	2283	SO:0001583	missense	645090	exon7			GCATTGAAATACC		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.41A>C	X.37:g.36317108A>C	ENSP00000367926:p.Glu14Ala	120.0	0.0	0		150.0	59.0	0.393333	NM_001098843		Missense_Mutation	SNP	ENST00000378657.4	37	CCDS55396.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.273007	0.40194	.	.	ENSG00000205081	ENST00000378653;ENST00000378657	T;T	0.27104	1.72;1.69	5.04	5.04	0.67666	.	.	.	.	.	T	0.30665	0.0772	N	0.24115	0.695	0.23174	N	0.99817	D	0.63046	0.992	P	0.60541	0.876	T	0.10567	-1.0624	9	0.30078	T	0.28	.	10.3241	0.43783	1.0:0.0:0.0:0.0	.	14	A6PW82	CX030_HUMAN	A	299;14	ENSP00000367922:E299A;ENSP00000367926:E14A	ENSP00000367922:E299A	E	+	2	0	CXorf30	36227029	1.000000	0.71417	0.426000	0.26672	0.079000	0.17450	4.858000	0.62947	1.776000	0.52262	0.486000	0.48141	GAA	.	.	none		0.358	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
UTP14A	10813	hgsc.bcm.edu	37	X	129045815	129045815	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:129045815G>A	ENST00000394422.3	+	6	483	c.455G>A	c.(454-456)cGg>cAg	p.R152Q	UTP14A_ENST00000371042.3_5'Flank|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000371051.5_Missense_Mutation_p.R98Q|UTP14A_ENST00000425117.2_Intron	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	152					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						CTGAAGAACCGGCAGGCAGAG	0.507																																					p.R152Q		Atlas-SNP	.											.	UTP14A	74	.	0			c.G455A						PASS	.						90.0	86.0	87.0					X																	129045815		2203	4300	6503	SO:0001583	missense	10813	exon6			AGAACCGGCAGGC	AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"""serologically defined colon cancer antigen 16"""	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.455G>A	X.37:g.129045815G>A	ENSP00000377944:p.Arg152Gln	66.0	0.0	0		66.0	17.0	0.257576	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Missense_Mutation	SNP	ENST00000394422.3	37	CCDS14615.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418778	0.25552	.	.	ENSG00000156697	ENST00000394422;ENST00000371051	T;T	0.30981	1.51;1.51	5.43	5.43	0.79202	.	0.173156	0.53938	D	0.000060	T	0.43787	0.1263	M	0.87682	2.9	0.80722	D	1	B;B	0.26258	0.145;0.019	B;B	0.20577	0.018;0.03	T	0.48068	-0.9067	10	0.56958	D	0.05	-5.4583	18.3408	0.90304	0.0:0.0:1.0:0.0	.	98;152	F8WD00;Q9BVJ6	.;UT14A_HUMAN	Q	152;98	ENSP00000377944:R152Q;ENSP00000360090:R98Q	ENSP00000360090:R98Q	R	+	2	0	UTP14A	128873496	1.000000	0.71417	0.986000	0.45419	0.160000	0.22226	3.602000	0.54066	2.270000	0.75569	0.411000	0.27672	CGG	.	.	none		0.507	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649	
CDC25C	995	hgsc.bcm.edu	37	5	137627769	137627769	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:137627769G>C	ENST00000323760.6	-	8	930	c.652C>G	c.(652-654)Cca>Gca	p.P218A	CDC25C_ENST00000348983.3_Missense_Mutation_p.P145A|CDC25C_ENST00000356505.3_Missense_Mutation_p.P188A|CDC25C_ENST00000513970.1_Missense_Mutation_p.P218A|CDC25C_ENST00000514555.1_Missense_Mutation_p.P188A|CDC25C_ENST00000415130.2_Missense_Mutation_p.P145A|CDC25C_ENST00000357274.3_Missense_Mutation_p.P175A	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	218					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AAGTTCTCTGGCATCGACGGG	0.443																																					p.P218A		Atlas-SNP	.											.	CDC25C	37	.	0			c.C652G						PASS	.						145.0	150.0	148.0					5																	137627769		2203	4300	6503	SO:0001583	missense	995	exon8			TCTCTGGCATCGA	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.652C>G	5.37:g.137627769G>C	ENSP00000321656:p.Pro218Ala	97.0	0.0	0		91.0	32.0	0.351648	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.68|15.68	2.905323|2.905323	0.52333|0.52333	.|.	.|.	ENSG00000158402|ENSG00000158402	ENST00000514017|ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022	.|T;T;T;T;T;T;T;T	.|0.34275	.|1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.37	3.09|3.09	3.09|3.09	0.35607|0.35607	.|.	.|0.258164	.|0.31461	.|N	.|0.007614	T|T	0.54695|0.54695	0.1874|0.1874	M|M	0.62723|0.62723	1.935|1.935	0.33220|0.33220	D|D	0.554573|0.554573	.|D;D;D;D	.|0.76494	.|0.974;0.987;0.999;0.979	.|P;P;D;P	.|0.80764	.|0.747;0.747;0.994;0.836	T|T	0.67150|0.67150	-0.5743|-0.5743	5|10	.|0.51188	.|T	.|0.08	-7.2435|-7.2435	14.0879|14.0879	0.64971|0.64971	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|235;188;145;218	.|G3V1P6;P30307-2;P30307-4;P30307	.|.;.;.;MPIP3_HUMAN	G|A	12|218;188;175;145;145;218;235;188;218	.|ENSP00000321656:P218A;ENSP00000348898:P188A;ENSP00000349821:P175A;ENSP00000345205:P145A;ENSP00000392631:P145A;ENSP00000424795:P218A;ENSP00000425470:P188A;ENSP00000427251:P218A	.|ENSP00000321656:P218A	A|P	-|-	2|1	0|0	CDC25C|CDC25C	137655668|137655668	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.412000|0.412000	0.31113|0.31113	4.268000|4.268000	0.58883|0.58883	2.012000|2.012000	0.59069|0.59069	0.557000|0.557000	0.71058|0.71058	GCC|CCA	.	.	none		0.443	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
MAN1C1	57134	hgsc.bcm.edu	37	1	26110236	26110236	+	Missense_Mutation	SNP	G	G	A	rs79507311	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26110236G>A	ENST00000374332.4	+	12	2179	c.1849G>A	c.(1849-1851)Gtg>Atg	p.V617M	MAN1C1_ENST00000263979.3_Missense_Mutation_p.V437M|MAN1C1_ENST00000374329.1_Missense_Mutation_p.V388M	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	617					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		CCCACTCCCGGTGAACCACTC	0.627													G|||	31	0.0061901	0.0008	0.0043	5008	,	,		17272	0.001		0.0239	False		,,,				2504	0.002				p.V617M		Atlas-SNP	.											.	MAN1C1	48	.	0			c.G1849A						PASS	.	G	MET/VAL	6,4400	11.4+/-27.6	0,6,2197	54.0	53.0	53.0		1849	2.3	0.0	1	dbSNP_131	53	119,8481	62.4+/-124.4	1,117,4182	yes	missense	MAN1C1	NM_020379.2	21	1,123,6379	AA,AG,GG		1.3837,0.1362,0.9611	possibly-damaging	617/631	26110236	125,12881	2203	4300	6503	SO:0001583	missense	57134	exon12			CTCCCGGTGAACC	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.1849G>A	1.37:g.26110236G>A	ENSP00000363452:p.Val617Met	31.0	0.0	0		40.0	27.0	0.675	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	22	0.010073260073260074	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	18	0.023746701846965697	G	17.85	3.489365	0.64074	0.001362	0.013837	ENSG00000117643	ENST00000374332;ENST00000263979;ENST00000374329	T;T;T	0.73363	-0.74;-0.74;-0.74	5.25	2.26	0.28386	.	0.244180	0.34484	N	0.003930	T	0.74489	0.3723	M	0.84219	2.685	0.29541	N	0.852042	D	0.76494	0.999	D	0.76575	0.988	T	0.75013	-0.3467	10	0.59425	D	0.04	.	8.8057	0.34936	0.4815:0.0:0.5185:0.0	.	617	Q9NR34	MA1C1_HUMAN	M	617;437;388	ENSP00000363452:V617M;ENSP00000263979:V437M;ENSP00000363449:V388M	ENSP00000263979:V437M	V	+	1	0	MAN1C1	25982823	0.892000	0.30473	0.027000	0.17364	0.975000	0.68041	1.342000	0.33919	0.182000	0.20032	0.561000	0.74099	GTG	G|0.990;A|0.010	0.010	strong		0.627	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	
SLC6A13	6540	hgsc.bcm.edu	37	12	333237	333237	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:333237C>T	ENST00000343164.4	-	11	1284	c.1232G>A	c.(1231-1233)cGc>cAc	p.R411H	SLC6A13_ENST00000445055.2_Missense_Mutation_p.R319H|SLC6A13_ENST00000539668.1_5'UTR	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	411					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GTTCTTCTTGCGGAACACGTG	0.572																																					p.R411H		Atlas-SNP	.											.	SLC6A13	62	.	0			c.G1232A						PASS	.						122.0	102.0	109.0					12																	333237		2203	4300	6503	SO:0001583	missense	6540	exon11			TTCTTGCGGAACA	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1232G>A	12.37:g.333237C>T	ENSP00000339260:p.Arg411His	96.0	0.0	0		86.0	5.0	0.0581395	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644952	0.67358	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.75938	-0.98;-0.98	5.5	4.6	0.57074	.	0.000000	0.85682	D	0.000000	D	0.85004	0.5598	M	0.88842	2.985	0.80722	D	1	P;P;P	0.47545	0.897;0.778;0.778	P;P;P	0.53224	0.721;0.598;0.598	D	0.88041	0.2781	10	0.72032	D	0.01	.	15.5587	0.76219	0.1392:0.8608:0.0:0.0	.	319;390;411	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	H	319;390;411	ENSP00000407104:R319H;ENSP00000339260:R411H	ENSP00000318097:R390H	R	-	2	0	SLC6A13	203498	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	7.760000	0.85248	1.305000	0.44909	0.491000	0.48974	CGC	.	.	none		0.572	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
EPHB4	2050	hgsc.bcm.edu	37	7	100417879	100417879	+	Missense_Mutation	SNP	C	C	T	rs201531252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100417879C>T	ENST00000358173.3	-	5	1316	c.848G>A	c.(847-849)gGg>gAg	p.G283E	EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Missense_Mutation_p.G283E|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	283	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGGCAGGACCCTTCTCCTGA	0.592																																					p.G283E	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G848A						PASS	.						105.0	120.0	115.0					7																	100417879		2203	4300	6503	SO:0001583	missense	2050	exon5			CAGGACCCTTCTC	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.848G>A	7.37:g.100417879C>T	ENSP00000350896:p.Gly283Glu	49.0	0.0	0		46.0	24.0	0.521739	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	C	8.451	0.853099	0.17106	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.15256	2.44;2.44	5.35	4.47	0.54385	Tyrosine-protein kinase ephrin type A/B receptor-like (1);	0.120033	0.37437	N	0.002098	T	0.10937	0.0267	L	0.31476	0.935	0.32118	N	0.588384	B;B;B;B	0.16603	0.018;0.018;0.001;0.009	B;B;B;B	0.20184	0.025;0.028;0.003;0.014	T	0.19321	-1.0309	10	0.02654	T	1	.	11.4994	0.50428	0.0:0.912:0.0:0.088	.	283;283;283;283	B5A972;B5A970;Q96L35;P54760	.;.;.;EPHB4_HUMAN	E	283	ENSP00000353833:G283E;ENSP00000350896:G283E	ENSP00000350896:G283E	G	-	2	0	EPHB4	100255815	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	3.317000	0.51968	1.240000	0.43803	0.655000	0.94253	GGG	C|0.999;T|0.001	0.001	weak		0.592	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
GTPBP8	29083	hgsc.bcm.edu	37	3	112718352	112718352	+	Missense_Mutation	SNP	G	G	T	rs1054263	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112718352G>T	ENST00000383678.2	+	5	808	c.726G>T	c.(724-726)caG>caT	p.Q242H	GTPBP8_ENST00000467752.1_Missense_Mutation_p.Q131H|GTPBP8_ENST00000383677.3_Missense_Mutation_p.Q209H|GTPBP8_ENST00000473129.1_Missense_Mutation_p.Q92H	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	242	EngB-type G.		Q -> H (in dbSNP:rs1054263).		barrier septum assembly (GO:0000917)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	6						AAGTGCTTCAGATCCAGAAAT	0.279													G|||	235	0.0469249	0.1218	0.0245	5008	,	,		17422	0.003		0.0308	False		,,,				2504	0.0235				p.Q242H		Atlas-SNP	.											GTPBP8,lymph_node,lymphoid_neoplasm,0,1	GTPBP8	22	1	0			c.G726T						PASS	.	G	HIS/GLN,HIS/GLN	487,3917	228.1+/-243.1	31,425,1746	94.0	95.0	94.0		726,627	4.9	1.0	3	dbSNP_86	94	296,8298	107.4+/-168.2	5,286,4006	yes	missense,missense	GTPBP8	NM_014170.2,NM_138485.1	24,24	36,711,5752	TT,TG,GG		3.4443,11.0581,6.024	possibly-damaging,possibly-damaging	242/285,209/252	112718352	783,12215	2202	4297	6499	SO:0001583	missense	29083	exon5			GCTTCAGATCCAG	BC037163	CCDS33820.1, CCDS33821.1	3q13.2	2008-02-05			ENSG00000163607	ENSG00000163607			25007	protein-coding gene	gene with protein product							Standard	NM_014170		Approved	HSPC135	uc003dzn.3	Q8N3Z3	OTTHUMG00000159268	ENST00000383678.2:c.726G>T	3.37:g.112718352G>T	ENSP00000373176:p.Gln242His	247.0	0.0	0		180.0	73.0	0.405556	NM_014170	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Missense_Mutation	SNP	ENST00000383678.2	37	CCDS33820.1	85	0.03891941391941392	47	0.09552845528455285	13	0.03591160220994475	0	0.0	25	0.032981530343007916	G	13.81	2.347604	0.41599	0.110581	0.034443	ENSG00000163607	ENST00000383678;ENST00000383677;ENST00000305485;ENST00000467752;ENST00000473129	T;T;T;T	0.71817	2.5;-0.6;2.5;-0.6	5.81	4.93	0.64822	.	0.368391	0.29715	N	0.011388	T	0.03739	0.0106	L	0.57536	1.79	0.33973	D	0.646991	P;B	0.42123	0.771;0.391	B;B	0.43251	0.413;0.235	T	0.55425	-0.8143	10	0.52906	T	0.07	-9.4679	13.5676	0.61828	0.0756:0.0:0.9244:0.0	rs1054263;rs3194778;rs1054263	209;242	Q8N3Z3-2;Q8N3Z3	.;GTPB8_HUMAN	H	242;209;265;131;92	ENSP00000373176:Q242H;ENSP00000373175:Q209H;ENSP00000417632:Q131H;ENSP00000418514:Q92H	ENSP00000303802:Q265H	Q	+	3	2	GTPBP8	114201042	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	2.759000	0.47573	1.461000	0.47929	0.655000	0.94253	CAG	G|0.948;T|0.052	0.052	strong		0.279	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170	
BMP10	27302	hgsc.bcm.edu	37	2	69093413	69093413	+	Missense_Mutation	SNP	G	G	A	rs34008398	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:69093413G>A	ENST00000295379.1	-	2	783	c.625C>T	c.(625-627)Cgt>Tgt	p.R209C		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	209					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						TTTTGCCAACGTCTGATGGCA	0.498													G|||	19	0.00379393	0.0008	0.0014	5008	,	,		20267	0.0		0.0169	False		,,,				2504	0.0				p.R209C		Atlas-SNP	.											.	BMP10	70	.	0			c.C625T						PASS	.	G	CYS/ARG	13,4393	20.2+/-43.8	0,13,2190	141.0	120.0	128.0		625	4.6	1.0	2	dbSNP_126	128	100,8500	56.8+/-118.0	0,100,4200	yes	missense	BMP10	NM_014482.1	180	0,113,6390	AA,AG,GG		1.1628,0.2951,0.8688	possibly-damaging	209/425	69093413	113,12893	2203	4300	6503	SO:0001583	missense	27302	exon2			GCCAACGTCTGAT	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.625C>T	2.37:g.69093413G>A	ENSP00000295379:p.Arg209Cys	285.0	0.0	0		209.0	151.0	0.722488	NM_014482	Q53R17|Q6NTE0	Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	9	0.004120879120879121	1	0.0020325203252032522	0	0.0	0	0.0	8	0.010554089709762533	G	15.35	2.808940	0.50421	0.002951	0.011628	ENSG00000163217	ENST00000295379	T	0.69040	-0.37	5.44	4.57	0.56435	Transforming growth factor-beta, N-terminal (1);	0.338806	0.37095	N	0.002250	T	0.66684	0.2814	M	0.72353	2.195	0.58432	D	0.999999	D	0.55605	0.972	P	0.49597	0.616	T	0.76219	-0.3039	10	0.87932	D	0	.	15.5959	0.76578	0.0:0.1377:0.8622:0.0	rs34008398	209	O95393	BMP10_HUMAN	C	209	ENSP00000295379:R209C	ENSP00000295379:R209C	R	-	1	0	BMP10	68946917	0.998000	0.40836	0.997000	0.53966	0.334000	0.28698	5.487000	0.66863	1.527000	0.49086	-0.150000	0.13652	CGT	G|0.991;A|0.009	0.009	strong		0.498	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
PRKD1	5587	hgsc.bcm.edu	37	14	30066797	30066797	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:30066797G>A	ENST00000331968.5	-	16	2563	c.2334C>T	c.(2332-2334)agC>agT	p.S778S	PRKD1_ENST00000415220.2_Silent_p.S786S	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	778	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GGAATGTGCCGCTTAGGCTTA	0.463																																					p.S778S		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2334T						PASS	.						156.0	144.0	148.0					14																	30066797		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon16			TGTGCCGCTTAGG		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2334C>T	14.37:g.30066797G>A		126.0	0.0	0		143.0	29.0	0.202797	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			.	.	none		0.463	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
FASTKD2	22868	hgsc.bcm.edu	37	2	207632128	207632128	+	Silent	SNP	C	C	T	rs150195745		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207632128C>T	ENST00000236980.6	+	2	1059	c.711C>T	c.(709-711)caC>caT	p.H237H	MDH1B_ENST00000392214.2_5'Flank|FASTKD2_ENST00000402774.3_Silent_p.H237H|MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000374412.3_5'Flank|MDH1B_ENST00000449792.1_5'Flank|FASTKD2_ENST00000403094.3_Silent_p.H237H	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	237					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TCAGTCTTCACGCCATAGTGA	0.413																																					p.H237H		Atlas-SNP	.											.	FASTKD2	49	.	0			c.C711T						PASS	.	C	,,	1,4315		0,1,2157	84.0	82.0	83.0		711,711,711	-0.4	0.1	2	dbSNP_134	83	0,8568		0,0,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	,,	0,1,6441	TT,TC,CC		0.0,0.0232,0.0078	,,	237/711,237/711,237/711	207632128	1,12883	2158	4284	6442	SO:0001819	synonymous_variant	22868	exon2			TCTTCACGCCATA	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.711C>T	2.37:g.207632128C>T		55.0	0.0	0		49.0	25.0	0.510204	NM_001136193	Q9NVX6|Q9Y2H7	Silent	SNP	ENST00000236980.6	37	CCDS2371.1																																																																																			C|1.000;T|0.000	0.000	weak		0.413	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
POLQ	10721	hgsc.bcm.edu	37	3	121208294	121208294	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121208294C>T	ENST00000264233.5	-	16	3612	c.3484G>A	c.(3484-3486)Gct>Act	p.A1162T		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1162					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GCCTCAACAGCTACTCCTCTG	0.368								DNA polymerases (catalytic subunits)																													p.A1162T	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G3484A						PASS	.						186.0	185.0	185.0					3																	121208294		2203	4300	6503	SO:0001583	missense	10721	exon16			CAACAGCTACTCC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3484G>A	3.37:g.121208294C>T	ENSP00000264233:p.Ala1162Thr	178.0	0.0	0		150.0	38.0	0.253333	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	7.638	0.680344	0.14907	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.52983	0.64	5.25	4.36	0.52297	.	2.127980	0.01493	N	0.017160	T	0.41305	0.1153	L	0.27053	0.805	0.09310	N	1	B;B	0.29301	0.156;0.241	B;B	0.25140	0.026;0.058	T	0.36768	-0.9734	10	0.28530	T	0.3	.	13.2429	0.60008	0.0:0.8408:0.1592:0.0	.	1162;334	O75417;O75417-2	DPOLQ_HUMAN;.	T	785;1162;1298	ENSP00000264233:A1162T	ENSP00000264233:A1162T	A	-	1	0	POLQ	122690984	0.015000	0.18098	0.011000	0.14972	0.099000	0.18886	1.197000	0.32211	1.408000	0.46895	0.563000	0.77884	GCT	.	.	none		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
HIP1R	9026	hgsc.bcm.edu	37	12	123345296	123345296	+	Missense_Mutation	SNP	G	G	A	rs141813189	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:123345296G>A	ENST00000253083.4	+	28	2856	c.2731G>A	c.(2731-2733)Gca>Aca	p.A911T		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	911	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.|Important for actin binding.				receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CCACGAGATCGCAGCCAGCAC	0.672											OREG0022225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0	0.0029	5008	,	,		15132	0.0		0.002	False		,,,				2504	0.0051				p.A911T		Atlas-SNP	.											.	HIP1R	68	.	0			c.G2731A						PASS	.	G	THR/ALA	0,4406		0,0,2203	40.0	43.0	42.0		2731	5.5	1.0	12	dbSNP_134	42	8,8592	7.1+/-27.0	0,8,4292	yes	missense	HIP1R	NM_003959.1	58	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	probably-damaging	911/1069	123345296	8,12998	2203	4300	6503	SO:0001583	missense	9026	exon28			GAGATCGCAGCCA	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.2731G>A	12.37:g.123345296G>A	ENSP00000253083:p.Ala911Thr	145.0	0.0	0	1526	177.0	82.0	0.463277	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	36	5.718378	0.96839	0.0	9.3E-4	ENSG00000130787	ENST00000253083	T	0.50813	0.73	5.49	5.49	0.81192	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.68686	0.3028	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.70479	-0.4860	10	0.66056	D	0.02	-17.9631	18.989	0.92783	0.0:0.0:1.0:0.0	.	911	O75146	HIP1R_HUMAN	T	911	ENSP00000253083:A911T	ENSP00000253083:A911T	A	+	1	0	HIP1R	121911249	1.000000	0.71417	0.960000	0.40013	0.905000	0.53344	9.794000	0.99096	2.578000	0.87016	0.655000	0.94253	GCA	G|0.999;A|0.001	0.001	strong		0.672	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
TDP2	51567	hgsc.bcm.edu	37	6	24653283	24653283	+	Silent	SNP	T	T	C	rs11559067	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24653283T>C	ENST00000378198.4	-	6	905	c.735A>G	c.(733-735)ttA>ttG	p.L245L	TDP2_ENST00000545995.1_Silent_p.L275L|TDP2_ENST00000341060.3_Silent_p.L187L|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	245					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GCATTTTCTTTAAAACCATTT	0.428								Direct reversal of damage					T|||	60	0.0119808	0.003	0.0202	5008	,	,		17943	0.001		0.0318	False		,,,				2504	0.0092				p.L245L		Atlas-SNP	.											.	TDP2	29	.	0			c.A735G						PASS	.	T		39,4367	43.1+/-76.7	0,39,2164	212.0	222.0	219.0		735	-1.5	0.0	6	dbSNP_120	219	322,8278	113.5+/-173.5	7,308,3985	no	coding-synonymous	TDP2	NM_016614.2		7,347,6149	CC,CT,TT		3.7442,0.8852,2.7756		245/363	24653283	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			TTTCTTTAAAACC	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.735A>G	6.37:g.24653283T>C		74.0	0.0	0		86.0	74.0	0.860465	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	37	CCDS4557.1																																																																																			T|0.977;C|0.023	0.023	strong		0.428	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
CTAGE5	4253	hgsc.bcm.edu	37	14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	rs61742363	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39818076A>G	ENST00000280083.3	+	23	2457	c.2143A>G	c.(2143-2145)Aga>Gga	p.R715G	CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000348007.3_Missense_Mutation_p.R672G			O15320	CTGE5_HUMAN	CTAGE family, member 5	715	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		ATTCTTGAGAAGAGGACCTCC	0.532													A|||	27	0.00539137	0.0	0.0173	5008	,	,		14299	0.0		0.0149	False		,,,				2504	0.0				p.R720G		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A2158G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	125.0	130.0	129.0		2143,2107,2014,2056	3.1	1.0	14	dbSNP_129	129	156,8444	73.5+/-136.2	0,156,4144	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	0,172,6331	GG,GA,AA		1.814,0.3631,1.3225	probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/805,703/793,672/762,686/776	39818076	172,12834	2203	4300	6503	SO:0001583	missense	4253	exon23			TTGAGAAGAGGAC	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2143A>G	14.37:g.39818076A>G	ENSP00000280083:p.Arg715Gly	88.0	0.0	0		129.0	61.0	0.472868	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	A	14.78	2.638501	0.47153	0.003631	0.01814	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.4;2.37;2.36;2.91;2.63;2.64;2.36;3.17;2.36	5.64	3.12	0.35913	.	0.000000	0.37623	N	0.002009	T	0.12178	0.0296	M	0.83312	2.635	0.29744	N	0.83689	B;B;B;B;B	0.28713	0.22;0.181;0.22;0.181;0.22	B;B;B;B;B	0.29267	0.1;0.074;0.1;0.074;0.1	T	0.06588	-1.0818	9	.	.	.	.	11.6343	0.51194	0.6083:0.3917:0.0:0.0	rs61742363	720;672;715;643;703	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	G	1250;703;635;686;715;720;715;640;672;686	ENSP00000452252:R1250G;ENSP00000343897:R703G;ENSP00000450869:R635G;ENSP00000379468:R686G;ENSP00000339286:R715G;ENSP00000379462:R720G;ENSP00000280083:R715G;ENSP00000452562:R640G;ENSP00000343912:R672G;ENSP00000450449:R686G	.	R	+	1	2	CTAGE5;RP11-407N17.3	38887827	1.000000	0.71417	0.992000	0.48379	0.895000	0.52256	0.816000	0.27267	0.940000	0.37473	0.533000	0.62120	AGA	A|0.988;G|0.012	0.012	strong		0.532	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
S100A7A	338324	hgsc.bcm.edu	37	1	153390649	153390649	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153390649A>G	ENST00000368729.4	+	2	148	c.91A>G	c.(91-93)Agc>Ggc	p.S31G	S100A7A_ENST00000329256.2_Missense_Mutation_p.S31G|S100A7A_ENST00000368728.2_Missense_Mutation_p.S31G	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	31	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)			cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGAGAAGCCAAGCCTGCTGAC	0.488																																					p.S31G		Atlas-SNP	.											.	S100A7A	24	.	0			c.A91G						PASS	.						223.0	193.0	203.0					1																	153390649		2203	4300	6503	SO:0001583	missense	338324	exon2			AAGCCAAGCCTGC	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	21657	protein-coding gene	gene with protein product			"""S100 calcium binding protein A15"", ""S100 calcium binding protein A7-like 1"""	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.91A>G	1.37:g.153390649A>G	ENSP00000357718:p.Ser31Gly	155.0	0.0	0		184.0	47.0	0.255435	NM_176823	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	37	CCDS30872.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.021565	0.00414	.	.	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.09255	3.0;3.0;3.0	2.27	0.278	0.15673	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.00815	0.0027	N	0.00729	-1.24	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.47156	-0.9139	9	0.45353	T	0.12	.	4.5895	0.12299	0.3303:0.0:0.6697:0.0	.	31	Q86SG5	S1A7A_HUMAN	G	31	ENSP00000357718:S31G;ENSP00000357717:S31G;ENSP00000329008:S31G	ENSP00000329008:S31G	S	+	1	0	S100A7A	151657273	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.315000	0.19451	0.051000	0.15978	-0.353000	0.07706	AGC	.	.	none		0.488	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823	
HLX	3142	hgsc.bcm.edu	37	1	221057573	221057573	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:221057573C>T	ENST00000366903.6	+	4	2495	c.994C>T	c.(994-996)Cgg>Tgg	p.R332W	HLX_ENST00000549319.1_Missense_Mutation_p.R118W	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	332					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R332W(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		GATGAAGTGGCGGCACTCCAA	0.632																																					p.R332W		Atlas-SNP	.											HLX,NS,carcinoma,0,1	HLX	67	1	1	Substitution - Missense(1)	endometrium(1)	c.C994T						scavenged	.						36.0	41.0	39.0					1																	221057573		2202	4300	6502	SO:0001583	missense	3142	exon4			AAGTGGCGGCACT	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.994C>T	1.37:g.221057573C>T	ENSP00000355870:p.Arg332Trp	114.0	1.0	0.00877193		136.0	40.0	0.294118	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037543	0.75617	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;D;D	0.97665	-4.48;-4.48;-4.48	5.17	0.831	0.18860	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.52532	D	0.000061	D	0.98798	0.9595	H	0.96518	3.835	0.48632	D	0.999682	D	0.89917	1.0	D	0.97110	1.0	D	0.99632	1.0986	10	0.87932	D	0	-29.0787	14.4728	0.67529	0.6337:0.3663:0.0:0.0	.	332	Q14774	HLX_HUMAN	W	332;65;118	ENSP00000355870:R332W;ENSP00000408248:R65W;ENSP00000449882:R118W	ENSP00000355870:R332W	R	+	1	2	HLX	219124196	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	1.035000	0.30216	-0.022000	0.13986	-0.310000	0.09108	CGG	.	.	none		0.632	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
WNK1	65125	hgsc.bcm.edu	37	12	922913	922913	+	Missense_Mutation	SNP	T	T	C	rs200234585		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:922913T>C	ENST00000315939.6	+	2	1508	c.865T>C	c.(865-867)Tcc>Ccc	p.S289P	WNK1_ENST00000447667.2_Missense_Mutation_p.S289P|WNK1_ENST00000535572.1_Missense_Mutation_p.S289P|WNK1_ENST00000530271.2_Missense_Mutation_p.S289P|WNK1_ENST00000537687.1_Missense_Mutation_p.S289P	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTCCTGGGAATCCACAGTAAA	0.353																																					p.S289P	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T865C						PASS	.						110.0	104.0	106.0					12																	922913		2203	4300	6503	SO:0001583	missense	65125	exon2			TGGGAATCCACAG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.865T>C	12.37:g.922913T>C	ENSP00000313059:p.Ser289Pro	77.0	0.0	0		67.0	31.0	0.462687	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297998	0.81025	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.83	5.83	0.93111	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.72771	0.3502	L	0.41079	1.255	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.974	D;D;P	0.81914	0.992;0.995;0.899	T	0.75266	-0.3378	10	0.72032	D	0.01	-12.6206	16.1995	0.82060	0.0:0.0:0.0:1.0	.	289;289;289	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	P	289	ENSP00000441972:S289P;ENSP00000313059:S289P;ENSP00000444465:S289P;ENSP00000392542:S289P;ENSP00000433548:S289P	ENSP00000313059:S289P	S	+	1	0	WNK1	793174	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.072000	0.64389	2.220000	0.72140	0.459000	0.35465	TCC	.	.	weak		0.353	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
PRDM9	56979	hgsc.bcm.edu	37	5	23510038	23510038	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23510038C>A	ENST00000296682.3	+	4	385	c.203C>A	c.(202-204)gCc>gAc	p.A68D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	68	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGTCTCAGAGCCACTCGACCA	0.488										HNSCC(3;0.000094)																											p.A68D		Atlas-SNP	.											.	PRDM9	344	.	0			c.C203A						PASS	.						72.0	69.0	70.0					5																	23510038		1879	4115	5994	SO:0001583	missense	56979	exon4			TCAGAGCCACTCG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.203C>A	5.37:g.23510038C>A	ENSP00000296682:p.Ala68Asp	215.0	0.0	0		172.0	50.0	0.290698	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.381532	0.61845	.	.	ENSG00000164256	ENST00000502755;ENST00000296682	T;T	0.00848	5.62;5.62	3.79	3.79	0.43588	Krueppel-associated box (2);Krueppel-associated box-related (1);	.	.	.	.	T	0.03178	0.0093	L	0.45051	1.395	0.29855	N	0.828075	D	0.71674	0.998	D	0.77557	0.99	T	0.26087	-1.0113	9	0.87932	D	0	-2.7458	11.3346	0.49496	0.0:1.0:0.0:0.0	.	68	Q9NQV7	PRDM9_HUMAN	D	68	ENSP00000425471:A68D;ENSP00000296682:A68D	ENSP00000296682:A68D	A	+	2	0	PRDM9	23545795	0.973000	0.33851	1.000000	0.80357	0.801000	0.45260	0.979000	0.29500	2.130000	0.65690	0.609000	0.83330	GCC	.	.	none		0.488	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
OR6C76	390326	hgsc.bcm.edu	37	12	55820685	55820685	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:55820685T>G	ENST00000328314.3	+	1	648	c.648T>G	c.(646-648)acT>acG	p.T216T		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCTCCTATACTTACATCATCA	0.368																																					p.T216T		Atlas-SNP	.											.	OR6C76	98	.	0			c.T648G						PASS	.						99.0	91.0	93.0					12																	55820685		2203	4300	6503	SO:0001819	synonymous_variant	390326	exon1			CTATACTTACATC		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.648T>G	12.37:g.55820685T>G		116.0	0.0	0		154.0	50.0	0.324675	NM_001005183		Silent	SNP	ENST00000328314.3	37	CCDS31823.1																																																																																			.	.	none		0.368	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
MCF2L2	23101	hgsc.bcm.edu	37	3	182941927	182941927	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182941927T>C	ENST00000328913.3	-	19	2464	c.2167A>G	c.(2167-2169)Agg>Ggg	p.R723G	MCF2L2_ENST00000473233.1_Missense_Mutation_p.R723G	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	723	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CAGATTGCCCTAGCTCGGGGC	0.368																																					p.R723G		Atlas-SNP	.											.	MCF2L2	164	.	0			c.A2167G						PASS	.						151.0	156.0	154.0					3																	182941927		2203	4300	6503	SO:0001583	missense	23101	exon19			TTGCCCTAGCTCG	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2167A>G	3.37:g.182941927T>C	ENSP00000328118:p.Arg723Gly	96.0	0.0	0		77.0	4.0	0.0519481	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739040	0.49045	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.63096	-0.02;-0.02	4.61	2.23	0.28157	Dbl homology (DH) domain (5);	0.487586	0.22204	N	0.063187	T	0.42200	0.1192	L	0.27053	0.805	0.09310	N	1	B	0.33413	0.411	B	0.31495	0.131	T	0.38001	-0.9681	10	0.87932	D	0	.	4.2628	0.10749	0.0:0.1046:0.2079:0.6876	.	723	Q86YR7	MF2L2_HUMAN	G	723	ENSP00000328118:R723G;ENSP00000420070:R723G	ENSP00000328118:R723G	R	-	1	2	MCF2L2	184424621	0.001000	0.12720	0.019000	0.16419	0.998000	0.95712	0.880000	0.28159	0.875000	0.35847	0.460000	0.39030	AGG	.	.	none		0.368	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
NTF3	4908	hgsc.bcm.edu	37	12	5604064	5604064	+	Silent	SNP	T	T	C	rs200399901		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:5604064T>C	ENST00000331010.6	+	1	767	c.684T>C	c.(682-684)acT>acC	p.T228T	NTF3_ENST00000423158.3_Silent_p.T241T|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	228					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						GAGCACTGACTTCAGAGAACA	0.488													T|||	1	0.000199681	0.0	0.0	5008	,	,		15317	0.0		0.001	False		,,,				2504	0.0				p.T241T	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.T723C						PASS	.	T	,	0,4406		0,0,2203	66.0	55.0	59.0		723,684	2.2	1.0	12		59	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	NTF3	NM_001102654.1,NM_002527.4	,	0,6,6497	CC,CT,TT		0.0698,0.0,0.0461	,	241/271,228/258	5604064	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			ACTGACTTCAGAG		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"""Endogenous ligands"""	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.684T>C	12.37:g.5604064T>C		28.0	0.0	0		37.0	19.0	0.513514	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	37	CCDS8538.1																																																																																			T|0.999;C|0.001	0.001	strong		0.488	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1		
UHRF2	115426	hgsc.bcm.edu	37	9	6413640	6413640	+	Silent	SNP	G	G	A	rs540145571		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413640G>A	ENST00000276893.5	+	1	318	c.150G>A	c.(148-150)aaG>aaA	p.K50K	UHRF2_ENST00000381373.3_Silent_p.K50K|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	50	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		ACCGGGGCAAGCAGGTGAGGC	0.726													G|||	1	0.000199681	0.0008	0.0	5008	,	,		8973	0.0		0.0	False		,,,				2504	0.0				p.K50K		Atlas-SNP	.											.	UHRF2	50	.	0			c.G150A						PASS	.						12.0	15.0	14.0					9																	6413640		2199	4298	6497	SO:0001819	synonymous_variant	115426	exon1			GGGCAAGCAGGTG	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.150G>A	9.37:g.6413640G>A		24.0	0.0	0		16.0	7.0	0.4375	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.726	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
SETD4	54093	hgsc.bcm.edu	37	21	37420606	37420606	+	Splice_Site	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:37420606T>G	ENST00000399215.1	-	4	1668	c.296A>C	c.(295-297)aAg>aCg	p.K99T	SETD4_ENST00000481477.1_Intron|SETD4_ENST00000399201.1_Splice_Site_p.K75T|SETD4_ENST00000399212.1_Splice_Site_p.K75T|SETD4_ENST00000399205.1_Splice_Site_p.K75T|SETD4_ENST00000399207.1_Splice_Site_p.K99T|SETD4_ENST00000399208.2_Splice_Site_p.K99T|SETD4_ENST00000332131.4_Splice_Site_p.K99T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	99	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GGTCACTTACTTAGTAATGTA	0.463																																					p.K99T		Atlas-SNP	.											.	SETD4	37	.	0			c.A296C						PASS	.						368.0	302.0	324.0					21																	37420606		2203	4300	6503	SO:0001630	splice_region_variant	54093	exon5			ACTTACTTAGTAA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 27"", ""chromosome 21 open reading frame 18"""	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.296+1A>C	21.37:g.37420606T>G		63.0	0.0	0		71.0	15.0	0.211268	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.540882	0.45280	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131;ENST00000399205;ENST00000399208;ENST00000399201;ENST00000399207;ENST00000424303;ENST00000429161;ENST00000446166	T;T;T;T;T;T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45	5.25	2.89	0.33648	SET domain (1);	0.203653	0.52532	D	0.000080	T	0.11110	0.0271	L	0.34521	1.04	0.80722	D	1	B;B;B;P	0.36086	0.08;0.147;0.241;0.536	B;B;B;B	0.36378	0.077;0.061;0.202;0.223	T	0.21280	-1.0250	9	.	.	.	6.6449	5.4075	0.16330	0.0:0.152:0.1478:0.7002	.	75;99;75;99	A8MTS1;C9JWV5;Q9NVD3-3;Q9NVD3	.;.;.;SETD4_HUMAN	T	99;75;99;75;99;75;99;99;99;75	ENSP00000382163:K99T;ENSP00000382161:K75T;ENSP00000329189:K99T;ENSP00000382156:K75T;ENSP00000382159:K99T;ENSP00000382152:K75T;ENSP00000382158:K99T;ENSP00000399998:K99T;ENSP00000396837:K99T;ENSP00000413318:K75T	.	K	-	2	0	SETD4	36342476	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	1.283000	0.33237	0.345000	0.23873	0.460000	0.39030	AAG	.	.	none		0.463	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	Missense_Mutation
CLDN24	100132463	hgsc.bcm.edu	37	4	184243174	184243174	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:184243174G>T	ENST00000541814.1	-	1	405	c.406C>A	c.(406-408)Ccc>Acc	p.P136T	CLDN22_ENST00000323319.5_5'Flank	NM_001185149.1	NP_001172078.1	A6NM45	CLD24_HUMAN	claudin 24	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	4						CAAGAGACGGGAACCAGGGCT	0.562																																					p.P136T		Atlas-SNP	.											.	CLDN24	5	.	0			c.C406A						PASS	.																																			SO:0001583	missense	100132463	exon1			AGACGGGAACCAG		CCDS54824.1	4q35.1	2012-07-05			ENSG00000185758	ENSG00000185758			37200	protein-coding gene	gene with protein product			"""claudin 21"""	CLDN21		12736707	Standard	NM_001185149		Approved		uc021xva.1	A6NM45	OTTHUMG00000160628	ENST00000541814.1:c.406C>A	4.37:g.184243174G>T	ENSP00000438400:p.Pro136Thr	150.0	0.0	0		147.0	8.0	0.0544218	NM_001185149	F5H040	Missense_Mutation	SNP	ENST00000541814.1	37	CCDS54824.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.267154	0.59540	.	.	ENSG00000185758	ENST00000541814;ENST00000514470	D;D	0.88201	-2.35;-2.35	4.9	4.9	0.64082	.	0.053948	0.85682	D	0.000000	D	0.94781	0.8315	M	0.86573	2.825	0.43879	D	0.996494	.	.	.	.	.	.	D	0.95280	0.8385	8	0.62326	D	0.03	.	18.3277	0.90260	0.0:0.0:1.0:0.0	.	.	.	.	T	136;128	ENSP00000438400:P136T;ENSP00000422519:P128T	ENSP00000422519:P128T	P	-	1	0	CLDN24	184480168	1.000000	0.71417	0.108000	0.21378	0.896000	0.52359	5.020000	0.64066	2.574000	0.86865	0.549000	0.68633	CCC	.	.	none		0.562	CLDN24-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001714660	
WBSCR17	64409	hgsc.bcm.edu	37	7	71142240	71142240	+	Silent	SNP	G	G	A	rs77485397	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:71142240G>A	ENST00000333538.5	+	9	2083	c.1449G>A	c.(1447-1449)ccG>ccA	p.P483P	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	483	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ACCAGGGGCCGCTGGAGAACC	0.532													G|||	74	0.0147764	0.0151	0.0245	5008	,	,		17185	0.006		0.0	False		,,,				2504	0.0317				p.P483P		Atlas-SNP	.											WBSCR17,NS,carcinoma,+1,2	WBSCR17	208	2	0			c.G1449A						PASS	.	G		56,4350	54.9+/-90.9	0,56,2147	225.0	224.0	224.0		1449	-10.4	0.0	7	dbSNP_131	224	0,8600		0,0,4300	no	coding-synonymous	WBSCR17	NM_022479.1		0,56,6447	AA,AG,GG		0.0,1.271,0.4306		483/599	71142240	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon9			GGGGCCGCTGGAG	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1449G>A	7.37:g.71142240G>A		45.0	0.0	0		49.0	25.0	0.510204	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																			G|0.995;A|0.005	0.005	strong		0.532	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
TLR4	7099	hgsc.bcm.edu	37	9	120476365	120476365	+	Silent	SNP	G	G	A	rs5030721	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:120476365G>A	ENST00000355622.6	+	3	2060	c.1959G>A	c.(1957-1959)aaG>aaA	p.K653K	TLR4_ENST00000394487.4_Silent_p.K613K|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	653					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TGGTCTATAAGTTCTATTTTC	0.418													G|||	24	0.00479233	0.0008	0.0014	5008	,	,		20759	0.001		0.0099	False		,,,				2504	0.0112				p.K653K		Atlas-SNP	.											.	TLR4	220	.	0			c.G1959A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	158.0	139.0	145.0		1959	1.0	1.0	9	dbSNP_113	145	99,8501	54.0+/-114.7	0,99,4201	no	coding-synonymous	TLR4	NM_138554.3		0,107,6396	AA,AG,GG		1.1512,0.1816,0.8227		653/840	120476365	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	7099	exon3			CTATAAGTTCTAT	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1959G>A	9.37:g.120476365G>A		57.0	0.0	0		61.0	24.0	0.393443	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Silent	SNP	ENST00000355622.6	37	CCDS6818.1																																																																																			G|0.993;A|0.007	0.007	strong		0.418	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
UTP20	27340	hgsc.bcm.edu	37	12	101755803	101755803	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101755803G>A	ENST00000261637.4	+	44	5929	c.5755G>A	c.(5755-5757)Gga>Aga	p.G1919R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1919					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GCTGCAGGTCGGAGATTTGGA	0.388																																					p.G1919R		Atlas-SNP	.											.	UTP20	222	.	0			c.G5755A						PASS	.						179.0	179.0	179.0					12																	101755803		2203	4300	6503	SO:0001583	missense	27340	exon44			CAGGTCGGAGATT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5755G>A	12.37:g.101755803G>A	ENSP00000261637:p.Gly1919Arg	79.0	0.0	0		76.0	18.0	0.236842	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531664	0.64972	.	.	ENSG00000120800	ENST00000261637	T	0.49139	0.79	6.03	5.15	0.70609	Armadillo-type fold (1);	0.048326	0.85682	N	0.000000	T	0.72447	0.3461	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.77688	-0.2494	10	0.56958	D	0.05	-12.7347	15.3525	0.74399	0.0666:0.0:0.9334:0.0	.	1919	O75691	UTP20_HUMAN	R	1919	ENSP00000261637:G1919R	ENSP00000261637:G1919R	G	+	1	0	UTP20	100279934	1.000000	0.71417	0.875000	0.34327	0.271000	0.26615	7.008000	0.76341	1.557000	0.49525	-0.140000	0.14226	GGA	.	.	none		0.388	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
DDR2	4921	hgsc.bcm.edu	37	1	162729613	162729613	+	Silent	SNP	C	C	T	rs56351141	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:162729613C>T	ENST00000367922.3	+	9	1137	c.699C>T	c.(697-699)acC>acT	p.T233T	DDR2_ENST00000367921.3_Silent_p.T233T	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	233					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	GCCAATTGACCGATGGTGTGT	0.537													C|||	27	0.00539137	0.0015	0.0115	5008	,	,		17195	0.0		0.0119	False		,,,				2504	0.0051				p.T233T	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											DDR2_ENST00000367922,right_upper_lobe,carcinoma,0,2	DDR2	228	2	0			c.C699T						PASS	.	C	,	9,4397	16.8+/-37.8	0,9,2194	102.0	89.0	94.0		699,699	-8.8	0.7	1	dbSNP_129	94	119,8481	62.1+/-124.0	1,117,4182	no	coding-synonymous,coding-synonymous	DDR2	NM_001014796.1,NM_006182.2	,	1,126,6376	TT,TC,CC		1.3837,0.2043,0.9842	,	233/856,233/856	162729613	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	4921	exon9			ATTGACCGATGGT	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.699C>T	1.37:g.162729613C>T		107.0	0.0	0		82.0	29.0	0.353659	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																			C|0.991;T|0.009	0.009	strong		0.537	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
CCDC146	57639	hgsc.bcm.edu	37	7	76866265	76866265	+	Splice_Site	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76866265T>C	ENST00000285871.4	+	3	285	c.158T>C	c.(157-159)tTa>tCa	p.L53S	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	53										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				CTTTGCTAGTTACATGCTATG	0.398																																					p.L53S		Atlas-SNP	.											.	CCDC146	87	.	0			c.T158C						PASS	.						170.0	130.0	144.0					7																	76866265		2203	4300	6503	SO:0001630	splice_region_variant	57639	exon3			GCTAGTTACATGC	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.157-1T>C	7.37:g.76866265T>C		81.0	0.0	0		69.0	30.0	0.434783	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.418000	0.62622	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D;D	0.84660	-1.88;-1.88	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000006	D	0.91872	0.7427	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.92425	0.5949	10	0.59425	D	0.04	-0.1732	15.6441	0.77033	0.0:0.0:0.0:1.0	.	53;53	Q8IYE0;C9JRR4	CC146_HUMAN;.	S	53	ENSP00000388649:L53S;ENSP00000285871:L53S	ENSP00000285871:L53S	L	+	2	0	AC007000.1	76704201	0.998000	0.40836	0.895000	0.35142	0.514000	0.34195	5.404000	0.66344	2.238000	0.73509	0.477000	0.44152	TTA	.	.	none		0.398	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	Missense_Mutation
PCIF1	63935	hgsc.bcm.edu	37	20	44574722	44574722	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44574722C>T	ENST00000372409.3	+	13	1760	c.1396C>T	c.(1396-1398)Ccc>Tcc	p.P466S	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	466					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						GAGGTTCCTGCCCCGGGTCTG	0.632																																					p.P466S		Atlas-SNP	.											.	PCIF1	51	.	0			c.C1396T						PASS	.						127.0	120.0	122.0					20																	44574722		2203	4300	6503	SO:0001583	missense	63935	exon13			TTCCTGCCCCGGG	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 121"""		"""chromosome 20 open reading frame 67"""	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1396C>T	20.37:g.44574722C>T	ENSP00000361486:p.Pro466Ser	61.0	0.0	0		83.0	22.0	0.26506	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	C	9.569	1.120426	0.20877	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.14	5.14	0.70334	Phosphorylated CTD interacting factor 1, WW domain (1);	0.168415	0.56097	D	0.000036	T	0.29491	0.0735	N	0.04768	-0.165	0.38097	D	0.937137	B	0.21688	0.059	B	0.22152	0.038	T	0.22138	-1.0225	9	0.20519	T	0.43	-14.9956	10.9093	0.47099	0.0:0.914:0.0:0.086	.	466	Q9H4Z3	PCIF1_HUMAN	S	466	.	ENSP00000361486:P466S	P	+	1	0	PCIF1	44008129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.613000	0.54152	2.696000	0.92011	0.456000	0.33151	CCC	.	.	none		0.632	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104	
NMUR2	56923	hgsc.bcm.edu	37	5	151777633	151777633	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:151777633T>G	ENST00000255262.3	-	2	964	c.799A>C	c.(799-801)Aac>Cac	p.N267H	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	267					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.N267H(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AGCATCTTGTTGACTGATTTT	0.398																																					p.N267H		Atlas-SNP	.											NMUR2,NS,carcinoma,0,1	NMUR2	111	1	1	Substitution - Missense(1)	lung(1)	c.A799C						PASS	.						138.0	131.0	133.0					5																	151777633		2203	4300	6503	SO:0001583	missense	56923	exon2			TCTTGTTGACTGA	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.799A>C	5.37:g.151777633T>G	ENSP00000255262:p.Asn267His	64.0	0.0	0		83.0	5.0	0.060241	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.588339	0.46110	.	.	ENSG00000132911	ENST00000255262	T	0.72051	-0.62	5.8	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.218017	0.40469	N	0.001094	T	0.67720	0.2923	L	0.48642	1.525	0.25169	N	0.990293	P	0.43938	0.822	P	0.44623	0.455	T	0.62134	-0.6918	10	0.56958	D	0.05	-12.0026	12.2618	0.54655	0.0:0.0:0.1421:0.8579	.	267	Q9GZQ4	NMUR2_HUMAN	H	267	ENSP00000255262:N267H	ENSP00000255262:N267H	N	-	1	0	NMUR2	151757826	1.000000	0.71417	0.985000	0.45067	0.451000	0.32288	2.866000	0.48420	0.990000	0.38787	0.477000	0.44152	AAC	.	.	none		0.398	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
HCN2	610	hgsc.bcm.edu	37	19	605093	605093	+	Silent	SNP	G	G	A	rs55839339	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:605093G>A	ENST00000251287.2	+	3	1142	c.1089G>A	c.(1087-1089)gcG>gcA	p.A363A		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	363					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGCCAGCGCGGTGATGAGGA	0.642													g|||	35	0.00698882	0.003	0.0159	5008	,	,		9413	0.002		0.0139	False		,,,				2504	0.0041				p.A363A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.G1089A						PASS	.	G		34,4372		0,34,2169	89.0	73.0	79.0		1089	-6.8	0.8	19	dbSNP_129	79	170,8424		3,164,4130	no	coding-synonymous	HCN2	NM_001194.3		3,198,6299	AA,AG,GG		1.9781,0.7717,1.5692		363/890	605093	204,12796	2203	4297	6500	SO:0001819	synonymous_variant	610	exon3			CAGCGCGGTGATG	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1089G>A	19.37:g.605093G>A		82.0	0.0	0		72.0	34.0	0.472222	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			G|0.984;A|0.016	0.016	strong		0.642	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249972	3249972	+	Missense_Mutation	SNP	C	C	A	rs200284450		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3249972C>A	ENST00000389832.5	-	2	364	c.58G>T	c.(58-60)Gat>Tat	p.D20Y	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.D19Y			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGGCCACATCCTCCTGGGCG	0.667																																					p.D20Y		Atlas-SNP	.											.	MRGPRE	35	.	0			c.G58T						PASS	.	C	TYR/ASP	4,3946		0,4,1971	39.0	43.0	42.0		55	2.8	0.1	11		42	3,8301		0,3,4149	yes	missense	MRGPRE	NM_001039165.2	160	0,7,6120	AA,AC,CC		0.0361,0.1013,0.0571	probably-damaging	19/312	3249972	7,12247	1975	4152	6127	SO:0001583	missense	116534	exon2			CCACATCCTCCTG	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.58G>T	11.37:g.3249972C>A	ENSP00000374482:p.Asp20Tyr	45.0	0.0	0		43.0	21.0	0.488372	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		.	.	.	.	.	.	.	.	.	.	c	14.72	2.620103	0.46736	0.001013	3.61E-4	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	2.83	2.83	0.33086	.	1.905200	0.03619	U	0.236065	T	0.17408	0.0418	N	0.08118	0	0.09310	N	1	P	0.49090	0.919	B	0.36989	0.238	T	0.25012	-1.0144	9	0.59425	D	0.04	-2.7001	8.884	0.35392	0.0:1.0:0.0:0.0	.	19	Q86SM8	MRGRE_HUMAN	Y	20;19	.	ENSP00000374482:D19Y	D	-	1	0	MRGPRE	3206548	0.057000	0.20700	0.062000	0.19696	0.065000	0.16274	2.890000	0.48609	1.399000	0.46721	0.484000	0.47621	GAT	.	.	weak		0.667	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
B4GALNT1	2583	hgsc.bcm.edu	37	12	58022555	58022555	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58022555C>T	ENST00000341156.4	-	8	1527	c.943G>A	c.(943-945)Gac>Aac	p.D315N	B4GALNT1_ENST00000550943.1_5'Flank|B4GALNT1_ENST00000449184.3_Missense_Mutation_p.D282N|B4GALNT1_ENST00000418555.2_Missense_Mutation_p.D260N	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	315					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			TCTGGCTTGTCGCTGTCGTCA	0.597																																					p.T315T		Atlas-SNP	.											.	B4GALNT1	53	.	0			c.A943A						PASS	.						81.0	66.0	71.0					12																	58022555		2203	4300	6503	SO:0001583	missense	2583	exon8			GCTTGTCGCTGTC	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	4117	protein-coding gene	gene with protein product	"""GD2 synthase, GM2 synthase"""	601873	"""UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)"", ""UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1"", ""spastic paraplegia 26"""	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.943G>A	12.37:g.58022555C>T	ENSP00000341562:p.Asp315Asn	91.0	0.0	0		69.0	26.0	0.376812	NM_001478	B4DE26|Q8N636	Silent	SNP	ENST00000341156.4	37	CCDS8950.1	.	.	.	.	.	.	.	.	.	.	.	18.01	3.527774	0.64860	.	.	ENSG00000135454	ENST00000341156;ENST00000418555	T;T	0.61392	0.11;0.11	4.89	4.89	0.63831	Glycosyl transferase, family 2 (1);	0.175267	0.49916	D	0.000137	T	0.38401	0.1039	N	0.20685	0.6	0.80722	D	1	P;P;P	0.42961	0.683;0.545;0.795	B;B;B	0.34452	0.115;0.055;0.183	T	0.34750	-0.9816	10	0.37606	T	0.19	-4.0522	13.3333	0.60503	0.0:0.8402:0.1598:0.0	.	282;260;315	B4DSP5;B4DE26;Q00973	.;.;B4GN1_HUMAN	N	315;260	ENSP00000341562:D315N;ENSP00000401601:D260N	ENSP00000341562:D315N	D	-	1	0	B4GALNT1	56308822	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	3.646000	0.54396	2.559000	0.86315	0.655000	0.94253	GAC	.	.	none		0.597	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156928576	156928576	+	Missense_Mutation	SNP	C	C	T	rs142957547	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156928576C>T	ENST00000361409.2	-	16	2082	c.1340G>A	c.(1339-1341)cGc>cAc	p.R447H	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R487H	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	447	RGSL. {ECO:0000255|PROSITE- ProRule:PRU00171}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGCCACTTGGCGCTCTCGGAG	0.537													C|||	8	0.00159744	0.0	0.0014	5008	,	,		19364	0.0		0.004	False		,,,				2504	0.0031				p.R487H		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G1460A						PASS	.	C	HIS/ARG,HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	49.0	45.0	46.0		1340,1460	4.1	1.0	1	dbSNP_134	46	42,8558	27.4+/-76.7	0,42,4258	yes	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	29,29	0,44,6459	TT,TC,CC		0.4884,0.0454,0.3383	benign,benign	447/1523,487/1563	156928576	44,12962	2203	4300	6503	SO:0001583	missense	9826	exon17			ACTTGGCGCTCTC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.1340G>A	1.37:g.156928576C>T	ENSP00000354644:p.Arg447His	131.0	0.0	0		134.0	58.0	0.432836	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	18.83	3.706799	0.68615	4.54E-4	0.004884	ENSG00000132694	ENST00000368194;ENST00000361409	D;D	0.86627	-2.15;-2.15	4.98	4.06	0.47325	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.222251	0.32055	N	0.006652	T	0.80454	0.4626	M	0.73962	2.25	0.80722	D	1	B;B	0.27013	0.162;0.166	B;B	0.22152	0.022;0.038	T	0.82137	-0.0606	10	0.66056	D	0.02	-8.7914	13.0194	0.58777	0.0:0.9212:0.0:0.0788	.	447;487	O15085;O15085-2	ARHGB_HUMAN;.	H	487;447	ENSP00000357177:R487H;ENSP00000354644:R447H	ENSP00000354644:R447H	R	-	2	0	ARHGEF11	155195200	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.468000	0.45102	1.334000	0.45468	0.491000	0.48974	CGC	C|0.996;T|0.004	0.004	strong		0.537	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
DPYSL5	56896	hgsc.bcm.edu	37	2	27121394	27121394	+	Silent	SNP	G	G	A	rs79644076	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27121394G>A	ENST00000288699.6	+	2	185	c.27G>A	c.(25-27)agG>agA	p.R9R	DPYSL5_ENST00000401478.1_Silent_p.R9R	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	9					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGCGTGAGGATCCTCATCA	0.547													G|||	7	0.00139776	0.0	0.0014	5008	,	,		23911	0.0		0.005	False		,,,				2504	0.001				p.R9R		Atlas-SNP	.											.	DPYSL5	69	.	0			c.G27A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	218.0	196.0	203.0		27	4.6	1.0	2	dbSNP_132	203	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	DPYSL5	NM_020134.3		0,85,6418	AA,AG,GG		0.8721,0.227,0.6535		9/565	27121394	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	56896	exon2			CGTGAGGATCCTC	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.27G>A	2.37:g.27121394G>A		213.0	1.0	0.00469484		223.0	110.0	0.493274	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			G|0.995;A|0.005	0.005	strong		0.547	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134	
AK8	158067	hgsc.bcm.edu	37	9	135703450	135703450	+	Missense_Mutation	SNP	G	G	T	rs114347984	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135703450G>T	ENST00000298545.3	-	7	1027	c.506C>A	c.(505-507)aCg>aAg	p.T169K	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	169	Adenylate kinase 1.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						GATCAGGACCGTGTCTGGAGC	0.547													G|||	10	0.00199681	0.0076	0.0	5008	,	,		19731	0.0		0.0	False		,,,				2504	0.0				p.T169K		Atlas-SNP	.											.	AK8	45	.	0			c.C506A						PASS	.	G	LYS/THR	38,4368		0,38,2165	74.0	53.0	60.0		506	1.8	0.0	9	dbSNP_132	60	6,8592		0,6,4293	yes	missense	AK8	NM_152572.2	78	0,44,6458	TT,TG,GG		0.0698,0.8625,0.3384	benign	169/480	135703450	44,12960	2203	4299	6502	SO:0001583	missense	158067	exon7			AGGACCGTGTCTG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.506C>A	9.37:g.135703450G>T	ENSP00000298545:p.Thr169Lys	55.0	0.0	0		49.0	18.0	0.367347	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	37	CCDS6954.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	9.781	1.175339	0.21704	0.008625	6.98E-4	ENSG00000165695	ENST00000298545	T	0.39997	1.05	5.78	1.84	0.25277	.	0.528145	0.21938	N	0.066940	T	0.28433	0.0703	L	0.53249	1.67	0.19775	N	0.999957	B	0.32939	0.391	B	0.38655	0.278	T	0.19257	-1.0311	10	0.17832	T	0.49	-9.7495	8.0442	0.30540	0.403:0.0:0.597:0.0	.	169	Q96MA6	KAD8_HUMAN	K	169	ENSP00000298545:T169K	ENSP00000298545:T169K	T	-	2	0	AK8	134693271	0.041000	0.20044	0.007000	0.13788	0.018000	0.09664	0.259000	0.18405	0.065000	0.16485	-0.244000	0.11960	ACG	G|0.997;T|0.003	0.003	strong		0.547	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
ACTG1	71	hgsc.bcm.edu	37	17	79479101	79479101	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479101A>T	ENST00000575842.1	-	2	617	c.191T>A	c.(190-192)aTc>aAc	p.I64N	ACTG1_ENST00000331925.2_Missense_Mutation_p.I64N|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.I64N|ACTG1_ENST00000575087.1_Missense_Mutation_p.I64N|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	64					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			CAGGGTCAGGATGCCACGCTT	0.637																																					p.I64N		Atlas-SNP	.											ACTG1,spleen,lymphoid_neoplasm,0,1	ACTG1	55	1	0			c.T191A						PASS	.						71.0	69.0	69.0					17																	79479101		2203	4300	6503	SO:0001583	missense	71	exon3			GTCAGGATGCCAC		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.191T>A	17.37:g.79479101A>T	ENSP00000458162:p.Ile64Asn	73.0	0.0	0		37.0	10.0	0.27027	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	A	7.994	0.753990	0.15778	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.90676	-2.71	3.88	3.88	0.44766	.	0.000000	0.64402	U	0.000002	D	0.90528	0.7032	M	0.83223	2.63	0.53688	D	0.999974	B	0.11235	0.004	B	0.20577	0.03	D	0.89491	0.3757	10	0.87932	D	0	.	11.8408	0.52353	1.0:0.0:0.0:0.0	.	64	P63261	ACTG_HUMAN	N	64	ENSP00000331514:I64N	ENSP00000331514:I64N	I	-	2	0	ACTG1	77093696	1.000000	0.71417	0.988000	0.46212	0.263000	0.26337	8.617000	0.90927	1.634000	0.50500	0.460000	0.39030	ATC	.	.	none		0.637	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111531387	111531387	+	Silent	SNP	A	A	T	rs149373122	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:111531387A>T	ENST00000261486.5	-	16	1671	c.1395T>A	c.(1393-1395)ggT>ggA	p.G465G	CTC-459M5.2_ENST00000515563.1_RNA|EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000506875.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	465						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CTGAATCTTCACCACTGTTAT	0.373													A|||	10	0.00199681	0.0	0.0058	5008	,	,		18453	0.0		0.005	False		,,,				2504	0.001				p.G465G		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.T1395A						PASS	.	A		8,3658		0,8,1825	113.0	103.0	106.0		1395	-2.2	1.0	5	dbSNP_134	106	77,8093		1,75,4009	no	coding-synonymous	EPB41L4A	NM_022140.3		1,83,5834	TT,TA,AA		0.9425,0.2182,0.7181		465/687	111531387	85,11751	1833	4085	5918	SO:0001819	synonymous_variant	64097	exon16			ATCTTCACCACTG	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1395T>A	5.37:g.111531387A>T		86.0	0.0	0		77.0	37.0	0.480519	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																			A|0.993;T|0.007	0.007	strong		0.373	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
OGDHL	55753	hgsc.bcm.edu	37	10	50944528	50944528	+	Missense_Mutation	SNP	C	C	A	rs140281439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50944528C>A	ENST00000374103.4	-	21	2714	c.2629G>T	c.(2629-2631)Gca>Tca	p.A877S	OGDHL_ENST00000432695.1_Missense_Mutation_p.A668S|OGDHL_ENST00000490844.1_5'UTR|OGDHL_ENST00000419399.1_Missense_Mutation_p.A820S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	877					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.A877T(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						GCCCGTGCTGCGGCCCCATCT	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		19100	0.0		0.002	False		,,,				2504	0.0				p.A877S		Atlas-SNP	.											OGDHL,NS,carcinoma,0,1	OGDHL	149	1	1	Substitution - Missense(1)	lung(1)	c.G2629T						PASS	.	C	SER/ALA,SER/ALA,SER/ALA	2,4404	4.2+/-10.8	0,2,2201	55.0	61.0	59.0		2458,2002,2629	5.4	0.1	10	dbSNP_134	59	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense,missense	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	99,99,99	0,26,6477	AA,AC,CC		0.2791,0.0454,0.1999	benign,benign,benign	820/954,668/802,877/1011	50944528	26,12980	2203	4300	6503	SO:0001583	missense	55753	exon21			GTGCTGCGGCCCC	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2629G>T	10.37:g.50944528C>A	ENSP00000363216:p.Ala877Ser	58.0	0.0	0		63.0	28.0	0.444444	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	12.90	2.076304	0.36662	4.54E-4	0.002791	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;T	0.10382	2.88;2.88;2.88	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	M	0.64404	1.975	0.80722	D	1	P;P;P	0.44281	0.831;0.726;0.74	P;P;B	0.50049	0.629;0.535;0.426	T	0.00443	-1.1736	10	0.30078	T	0.28	.	19.1605	0.93529	0.0:1.0:0.0:0.0	.	820;668;877	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	S	877;820;668	ENSP00000363216:A877S;ENSP00000401356:A820S;ENSP00000390240:A668S	ENSP00000363216:A877S	A	-	1	0	OGDHL	50614534	1.000000	0.71417	0.113000	0.21522	0.092000	0.18411	7.818000	0.86416	2.538000	0.85594	0.484000	0.47621	GCA	C|0.998;A|0.002	0.002	strong		0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
BTG1	694	hgsc.bcm.edu	37	12	92539189	92539189	+	Silent	SNP	G	G	A	rs201780644		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:92539189G>A	ENST00000256015.3	-	1	484	c.123C>T	c.(121-123)agC>agT	p.S41S	RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	41					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GCAGGCTCTGGCTGAAGGTCT	0.692			T	MYC	BCLL								G|||	1	0.000199681	0.0	0.0014	5008	,	,		11116	0.0		0.0	False		,,,				2504	0.0				p.S41S		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.C123T						PASS	.						34.0	36.0	35.0					12																	92539189		2202	4299	6501	SO:0001819	synonymous_variant	694	exon1			GCTCTGGCTGAAG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.123C>T	12.37:g.92539189G>A		109.0	0.0	0		106.0	30.0	0.283019	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			G|1.000;A|0.000	0.000	strong		0.692	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
TSPEAR	54084	hgsc.bcm.edu	37	21	45949769	45949769	+	Silent	SNP	G	G	A	rs117791519	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45949769G>A	ENST00000323084.4	-	5	767	c.702C>T	c.(700-702)aaC>aaT	p.N234N	TSPEAR_ENST00000397916.1_Silent_p.N166N	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	234	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CCAGCGGGGCGTTCCTGCTGG	0.632													G|||	11	0.00219649	0.0015	0.0014	5008	,	,		17868	0.0		0.008	False		,,,				2504	0.0				p.N234N		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C702T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	40.0	45.0	44.0		702	-5.5	0.0	21	dbSNP_132	44	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	TSPEAR	NM_144991.2		0,55,6448	AA,AG,GG		0.593,0.0908,0.4229		234/670	45949769	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	54084	exon5			CGGGGCGTTCCTG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.702C>T	21.37:g.45949769G>A		36.0	0.0	0		57.0	40.0	0.701754	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			G|0.996;A|0.004	0.004	strong		0.632	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	3'UTR	SNP	A	A	G	rs1137282	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25362777A>G	ENST00000256078.4	-	0	706				KRAS_ENST00000311936.3_Silent_p.D173D|KRAS_ENST00000557334.1_Silent_p.D60D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			TCTTTTTACCATCTTTGCTCA	0.279		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			A|||	879	0.175519	0.18	0.1931	5008	,	,		18305	0.0923		0.2187	False		,,,				2504	0.1984				p.D173D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	.	KRAS	30930	.	0			c.T519C						PASS	.	A	,	753,3647	305.5+/-289.0	61,631,1508	68.0	64.0	65.0		519,	3.4	1.0	12	dbSNP_86	65	1853,6727	328.5+/-318.3	168,1517,2605	no	coding-synonymous,utr-3	KRAS	NM_004985.3,NM_033360.2	,	229,2148,4113	GG,GA,AA		21.5967,17.1136,20.077	,	173/189,	25362777	2606,10374	2200	4290	6490	SO:0001624	3_prime_UTR_variant	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TTTACCATCTTTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.*73T>C	12.37:g.25362777A>G		102.0	0.0	0		122.0	63.0	0.516393	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																			T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong		0.279	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
KMT2C	58508	hgsc.bcm.edu	37	7	151962183	151962183	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:151962183A>C	ENST00000262189.6	-	8	1342	c.1124T>G	c.(1123-1125)gTt>gGt	p.V375G	KMT2C_ENST00000355193.2_Missense_Mutation_p.V375G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	375					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TAATGGAGTAACCGCTATATC	0.448																																					p.V375G		Atlas-SNP	.											MLL3_ENST00000355193,right_upper_lobe,carcinoma,0,2	MLL3	1564	2	0			c.T1124G						scavenged	.						497.0	442.0	460.0					7																	151962183		2203	4300	6503	SO:0001583	missense	58508	exon8			GGAGTAACCGCTA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1124T>G	7.37:g.151962183A>C	ENSP00000262189:p.Val375Gly	245.0	0.0	0		288.0	20.0	0.0694444	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	9.892	1.204596	0.22205	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98958	-5.27;-5.27	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.203382	0.23918	U	0.043277	D	0.98349	0.9452	M	0.76170	2.325	0.80722	D	1	D	0.64830	0.994	P	0.52109	0.69	D	0.98139	1.0435	10	0.40728	T	0.16	.	14.395	0.67005	1.0:0.0:0.0:0.0	.	375	Q8NEZ4	MLL3_HUMAN	G	375	ENSP00000262189:V375G;ENSP00000347325:V375G	ENSP00000262189:V375G	V	-	2	0	MLL3	151593116	1.000000	0.71417	0.992000	0.48379	0.034000	0.12701	4.542000	0.60677	1.843000	0.53566	0.455000	0.32223	GTT	.	.	none		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
GORASP1	64689	hgsc.bcm.edu	37	3	39140352	39140352	+	Missense_Mutation	SNP	C	C	A	rs138864486	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39140352C>A	ENST00000319283.3	-	8	1770	c.949G>T	c.(949-951)Gac>Tac	p.D317Y	GORASP1_ENST00000479927.1_Missense_Mutation_p.D222Y|GORASP1_ENST00000422110.2_Missense_Mutation_p.D162Y|GORASP1_ENST00000476334.1_5'UTR	NM_031899.2	NP_114105.1	Q9BQQ3	GORS1_HUMAN	golgi reassembly stacking protein 1, 65kDa	317					Golgi organization (GO:0007030)|mitotic cell cycle (GO:0000278)|negative regulation of dendrite morphogenesis (GO:0050774)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(1)|ovary(3)|urinary_tract(1)	14				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		TTGCTGTTGTCCAAGAGAGAA	0.582													C|||	46	0.0091853	0.0	0.013	5008	,	,		19642	0.0		0.0089	False		,,,				2504	0.0286				p.D317Y		Atlas-SNP	.											.	GORASP1	42	.	0			c.G949T						PASS	.	C	TYR/ASP	7,4399	12.9+/-30.5	0,7,2196	100.0	91.0	94.0		949	4.7	1.0	3	dbSNP_134	94	83,8517	48.5+/-108.0	0,83,4217	yes	missense	GORASP1	NM_031899.2	160	0,90,6413	AA,AC,CC		0.9651,0.1589,0.692	probably-damaging	317/441	39140352	90,12916	2203	4300	6503	SO:0001583	missense	64689	exon8			TGTTGTCCAAGAG	AJ409349	CCDS2681.1, CCDS63596.1, CCDS63597.1	3p22-p21.33	2008-04-23	2002-08-29	2002-05-24	ENSG00000114745	ENSG00000114745			16769	protein-coding gene	gene with protein product		606867	"""golgi phosphoprotein 5"""	GOLPH5			Standard	NM_001278789		Approved	GRASP65, P65, FLJ23443	uc003ciw.1	Q9BQQ3	OTTHUMG00000131292	ENST00000319283.3:c.949G>T	3.37:g.39140352C>A	ENSP00000313869:p.Asp317Tyr	107.0	0.0	0		131.0	58.0	0.442748	NM_031899	B3KWC8|Q3SYG7|Q8N272|Q96H42	Missense_Mutation	SNP	ENST00000319283.3	37	CCDS2681.1	12	0.005494505494505495	0	0.0	6	0.016574585635359115	0	0.0	6	0.0079155672823219	C	19.94	3.920111	0.73098	0.001589	0.009651	ENSG00000114745	ENST00000319283;ENST00000422110;ENST00000479927	T;T;T	0.56275	0.66;0.47;0.56	4.68	4.68	0.58851	.	0.587157	0.18456	N	0.140696	T	0.53706	0.1813	M	0.65975	2.015	0.39515	D	0.96841	D;D;D	0.89917	0.996;1.0;0.989	P;D;P	0.71870	0.819;0.975;0.781	T	0.67229	-0.5723	10	0.72032	D	0.01	-29.4781	13.3563	0.60629	0.0:1.0:0.0:0.0	.	222;162;317	B4E1H8;B3KPY8;Q9BQQ3	.;.;GORS1_HUMAN	Y	317;162;222	ENSP00000313869:D317Y;ENSP00000395709:D162Y;ENSP00000419123:D222Y	ENSP00000313869:D317Y	D	-	1	0	GORASP1	39115356	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.606000	0.54095	2.608000	0.88229	0.650000	0.86243	GAC	C|0.993;A|0.007	0.007	strong		0.582	GORASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254060.1		
C3orf30	152405	hgsc.bcm.edu	37	3	118865647	118865647	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:118865647G>A	ENST00000295622.1	+	1	651	c.611G>A	c.(610-612)cGa>cAa	p.R204Q	IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	204										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		GAGGCTGAGCGAAGAACTTCT	0.517																																					p.R204Q		Atlas-SNP	.											C3orf30,NS,carcinoma,0,1	C3orf30	64	1	0			c.G611A						PASS	.						110.0	114.0	112.0					3																	118865647		2203	4300	6503	SO:0001583	missense	152405	exon1			CTGAGCGAAGAAC	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.611G>A	3.37:g.118865647G>A	ENSP00000295622:p.Arg204Gln	68.0	0.0	0		47.0	22.0	0.468085	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	G	9.048	0.991375	0.18966	.	.	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.23950	1.88	3.6	-3.75	0.04372	.	1.346930	0.05074	N	0.482208	T	0.16128	0.0388	N	0.24115	0.695	0.09310	N	1	B;B	0.22909	0.077;0.038	B;B	0.14578	0.006;0.011	T	0.29671	-1.0004	10	0.16896	T	0.51	-0.1891	11.8007	0.52124	0.7483:0.0:0.2517:0.0	.	204;204	E9PFE5;Q96M34	.;CC030_HUMAN	Q	204	ENSP00000295622:R204Q	ENSP00000295622:R204Q	R	+	2	0	C3orf30	120348337	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.508000	0.06344	-1.001000	0.03434	-0.351000	0.07748	CGA	.	.	none		0.517	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121435427G>A	ENST00000257555.6	+	7	1686	c.1460G>A	c.(1459-1461)aGc>aAc	p.S487N	HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N			P20823	HNF1A_HUMAN	HNF1 homeobox A	487			S -> N (in dbSNP:rs2464196). {ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGACCCAGAGCCCCTTCATG	0.637									Hepatic Adenoma, Familial Clustering of				g|||	1591	0.317692	0.112	0.3501	5008	,	,		18114	0.4732		0.3161	False		,,,				2504	0.4141				p.S487N		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1460A	GRCh37	CM067474	HNF1A	M	rs2464196	PASS	.	G	ASN/SER	541,3865	230.4+/-244.6	42,457,1704	29.0	28.0	29.0		1460	3.5	1.0	12	dbSNP_100	29	2676,5924	411.0+/-350.3	431,1814,2055	yes	missense	HNF1A	NM_000545.5	46	473,2271,3759	AA,AG,GG		31.1163,12.2787,24.7347	possibly-damaging	487/632	121435427	3217,9789	2203	4300	6503	SO:0001583	missense	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCCAGAGCCCCTT	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1460G>A	12.37:g.121435427G>A	ENSP00000257555:p.Ser487Asn	114.0	0.0	0		127.0	124.0	0.976378	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	715	0.3273809523809524	54	0.10975609756097561	132	0.36464088397790057	296	0.5174825174825175	233	0.3073878627968338	G	12.39	1.924644	0.34002	0.122787	0.311163	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000340577;ENST00000544413	D;D;D	0.97455	-4.39;-4.39;-4.39	4.49	3.53	0.40419	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.068781	0.64402	N	0.000014	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.99999999123403	B;B;B	0.24576	0.0;0.014;0.106	B;B;B	0.32533	0.005;0.085;0.147	T	0.04153	-1.0973	9	0.42905	T	0.14	-9.2011	10.4952	0.44772	0.104:0.0:0.896:0.0	rs2464196;rs2708085;rs16950667;rs17847503;rs56962510;rs2464196	487;487;487	F5H0K0;P20823;E7EUQ4	.;HNF1A_HUMAN;.	N	487;379;487;308;487;487;487	ENSP00000257555:S487N;ENSP00000443112:S487N;ENSP00000438804:S487N	ENSP00000257555:S487N	S	+	2	0	HNF1A	119919810	0.950000	0.32346	0.992000	0.48379	0.944000	0.59088	1.527000	0.35975	0.976000	0.38417	0.655000	0.94253	AGC	G|0.725;A|0.275	0.275	strong		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
SLC7A1	6541	hgsc.bcm.edu	37	13	30110256	30110256	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:30110256C>G	ENST00000380752.5	-	3	456	c.70G>C	c.(70-72)Gag>Cag	p.E24Q		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	24					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CGCGTCTCCTCCCGGCTACAG	0.587																																					p.E24Q		Atlas-SNP	.											.	SLC7A1	64	.	0			c.G70C						PASS	.						57.0	62.0	60.0					13																	30110256		2203	4300	6503	SO:0001583	missense	6541	exon3			TCTCCTCCCGGCT	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"""Solute carriers"""	11057	protein-coding gene	gene with protein product	"""ecotropic retroviral receptor"", ""amino acid transporter, cationic 1"""	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.70G>C	13.37:g.30110256C>G	ENSP00000370128:p.Glu24Gln	78.0	0.0	0		71.0	31.0	0.43662	NM_003045	Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	37	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.046474	0.36085	.	.	ENSG00000139514	ENST00000380752;ENST00000450494	D;D	0.88586	-2.17;-2.4	4.82	4.82	0.62117	.	0.054005	0.64402	D	0.000001	D	0.88500	0.6453	M	0.83012	2.62	0.48452	D	0.999658	B	0.33477	0.413	B	0.35770	0.21	D	0.85308	0.1077	10	0.24483	T	0.36	.	10.6286	0.45523	0.0:0.913:0.0:0.087	.	24	P30825	CTR1_HUMAN	Q	24	ENSP00000370128:E24Q;ENSP00000390092:E24Q	ENSP00000370128:E24Q	E	-	1	0	SLC7A1	29008256	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	5.803000	0.69129	2.504000	0.84457	0.655000	0.94253	GAG	.	.	none		0.587	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045	
PARVA	55742	hgsc.bcm.edu	37	11	12525965	12525965	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:12525965G>C	ENST00000550549.1	+	6	695	c.646G>C	c.(646-648)Gtt>Ctt	p.V216L	PARVA_ENST00000334956.8_Missense_Mutation_p.V256L|PARVA_ENST00000539723.1_Missense_Mutation_p.V216L|PARVA_ENST00000538608.1_Missense_Mutation_p.V163L			Q9NVD7	PARVA_HUMAN	parvin, alpha	216					actin cytoskeleton reorganization (GO:0031532)|actin-mediated cell contraction (GO:0070252)|cell junction assembly (GO:0034329)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|heterotypic cell-cell adhesion (GO:0034113)|outflow tract septum morphogenesis (GO:0003148)|regulation of cell shape (GO:0008360)|smooth muscle cell chemotaxis (GO:0071670)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)	11				Epithelial(150;0.00624)		CATCCAAGTGGTTGTGGTCCA	0.498																																					p.V256L		Atlas-SNP	.											.	PARVA	27	.	0			c.G766C						PASS	.						101.0	96.0	98.0					11																	12525965		2036	4169	6205	SO:0001583	missense	55742	exon6			CAAGTGGTTGTGG	AF237771	CCDS44541.1, CCDS44541.2	11p15.3	2014-06-13	2005-05-26		ENSG00000197702	ENSG00000197702		"""Parvins"""	14652	protein-coding gene	gene with protein product		608120	"""matrix-remodelling associated 2"""	MXRA2		11171322	Standard	NM_018222		Approved	FLJ12254, FLJ10793	uc001mki.4	Q9NVD7	OTTHUMG00000165778	ENST00000550549.1:c.646G>C	11.37:g.12525965G>C	ENSP00000447198:p.Val216Leu	160.0	0.0	0		131.0	63.0	0.480916	NM_018222	Q96C85|Q9HA48	Missense_Mutation	SNP	ENST00000550549.1	37		.	.	.	.	.	.	.	.	.	.	G	16.41	3.115564	0.56505	.	.	ENSG00000197702	ENST00000334956;ENST00000539723;ENST00000550549;ENST00000538608;ENST00000528916	T;T;T;T;T	0.70164	-0.46;-0.44;-0.44;0.16;0.16	5.03	5.03	0.67393	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.74313	0.3700	M	0.61703	1.905	0.80722	D	1	P;B	0.46512	0.879;0.303	P;B	0.52031	0.688;0.05	T	0.71777	-0.4490	10	0.33940	T	0.23	-19.2457	18.5136	0.90926	0.0:0.0:1.0:0.0	.	163;216	B7Z952;Q9NVD7	.;PARVA_HUMAN	L	256;216;216;163;180	ENSP00000334008:V256L;ENSP00000438967:V216L;ENSP00000447198:V216L;ENSP00000442960:V163L;ENSP00000435860:V180L	ENSP00000334008:V256L	V	+	1	0	PARVA	12482541	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.620000	0.83070	2.775000	0.95449	0.655000	0.94253	GTT	.	.	none		0.498	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222	
PKD1	5310	hgsc.bcm.edu	37	16	2164244	2164244	+	Missense_Mutation	SNP	G	G	A	rs139963923		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:2164244G>A	ENST00000262304.4	-	11	2988	c.2780C>T	c.(2779-2781)aCg>aTg	p.T927M	PKD1_ENST00000423118.1_Missense_Mutation_p.T927M|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	927	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTCCTCCGCCGTCACCCGCAG	0.677																																					p.T927M		Atlas-SNP	.											.	PKD1	184	.	0			c.C2780T						PASS	.	G	MET/THR,MET/THR	0,4338		0,0,2169	14.0	14.0	14.0		2780,2780	-5.7	0.0	16	dbSNP_134	14	1,8495		0,1,4247	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	81,81	0,1,6416	AA,AG,GG		0.0118,0.0,0.0078	possibly-damaging,possibly-damaging	927/4303,927/4304	2164244	1,12833	2169	4248	6417	SO:0001583	missense	5310	exon11			TCCGCCGTCACCC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.2780C>T	16.37:g.2164244G>A	ENSP00000262304:p.Thr927Met	78.0	0.0	0		63.0	24.0	0.380952	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	6.600	0.479161	0.12581	0.0	1.18E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.68903	-0.36;-0.36	4.96	-5.71	0.02413	Polycystin cation channel (1);	0.553584	0.18955	N	0.126571	T	0.32675	0.0837	N	0.12182	0.205	0.09310	N	1	B;B	0.30114	0.269;0.066	B;B	0.17979	0.02;0.008	T	0.10520	-1.0626	10	0.54805	T	0.06	.	1.975	0.03414	0.2493:0.0753:0.3095:0.3658	.	927;927	P98161-3;P98161	.;PKD1_HUMAN	M	927;927;642	ENSP00000262304:T927M;ENSP00000399501:T927M	ENSP00000262304:T927M	T	-	2	0	PKD1	2104245	0.001000	0.12720	0.001000	0.08648	0.192000	0.23643	-0.055000	0.11807	-0.792000	0.04480	-0.476000	0.04901	ACG	G|1.000;A|0.000	0.000	weak		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
VANGL1	81839	hgsc.bcm.edu	37	1	116206871	116206871	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116206871A>G	ENST00000355485.2	+	4	1065	c.794A>G	c.(793-795)tAc>tGc	p.Y265C	VANGL1_ENST00000310260.3_Missense_Mutation_p.Y265C|VANGL1_ENST00000369510.4_Missense_Mutation_p.Y263C|VANGL1_ENST00000369509.1_Missense_Mutation_p.Y265C	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	265					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TCCCGCTTCTACAGCCTGGGA	0.597																																					p.Y265C		Atlas-SNP	.											.	VANGL1	65	.	0			c.A794G						PASS	.						30.0	29.0	30.0					1																	116206871		2203	4299	6502	SO:0001583	missense	81839	exon4			GCTTCTACAGCCT	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"""vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)"", ""vang-like 1 (van gogh, Drosophila)"""			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.794A>G	1.37:g.116206871A>G	ENSP00000347672:p.Tyr265Cys	60.0	0.0	0		46.0	25.0	0.543478	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167639	0.78339	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.94039	0.8090	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95115	0.8241	10	0.87932	D	0	0.8661	16.3383	0.83074	1.0:0.0:0.0:0.0	.	263;265	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	C	265;263;265;265	ENSP00000347672:Y265C;ENSP00000358523:Y263C;ENSP00000310800:Y265C;ENSP00000358522:Y265C	ENSP00000310800:Y265C	Y	+	2	0	VANGL1	116008394	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.962000	0.93254	2.322000	0.78497	0.528000	0.53228	TAC	.	.	none		0.597	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1		
PIGT	51604	hgsc.bcm.edu	37	20	44048224	44048224	+	Silent	SNP	T	T	C	rs147475258		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44048224T>C	ENST00000279036.6	+	5	755	c.675T>C	c.(673-675)gtT>gtC	p.V225V	PIGT_ENST00000535404.1_Silent_p.V70V|PIGT_ENST00000341555.5_Intron|PIGT_ENST00000543458.2_Silent_p.V169V|PIGT_ENST00000279035.9_Silent_p.V123V|PIGT_ENST00000372689.5_Silent_p.V225V|PIGT_ENST00000545755.1_5'UTR	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	225					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				TCCGCCCTGTTTGCAGAGTAA	0.552													T|||	1	0.000199681	0.0008	0.0	5008	,	,		20797	0.0		0.0	False		,,,				2504	0.0				p.V225V		Atlas-SNP	.											.	PIGT	85	.	0			c.T675C						PASS	.	T	,,,	1,4405	2.1+/-5.4	0,1,2202	111.0	99.0	103.0		507,675,369,675	-2.1	0.4	20	dbSNP_134	103	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIGT	NM_001184728.1,NM_001184729.1,NM_001184730.1,NM_015937.4	,,,	0,28,6475	CC,CT,TT		0.314,0.0227,0.2153	,,,	169/523,225/512,123/477,225/579	44048224	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	51604	exon5			CCCTGTTTGCAGA		CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"""Phosphatidylinositol glycan anchor biosynthesis"""	14938	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610272	"""phosphatidylinositol glycan, class T"""			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.675T>C	20.37:g.44048224T>C		57.0	0.0	0		88.0	35.0	0.397727	NM_001184729	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Silent	SNP	ENST00000279036.6	37	CCDS13353.1																																																																																			T|0.999;C|0.001	0.001	strong		0.552	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937	
CYP2A7	1549	hgsc.bcm.edu	37	19	41382544	41382544	+	Silent	SNP	G	G	A	rs116333747	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41382544G>A	ENST00000301146.4	-	8	1732	c.1191C>T	c.(1189-1191)tcC>tcT	p.S397S	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Silent_p.S346S	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	397						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CTCTCAGCACGGAGCCCAGCA	0.552													.|||	29	0.00579073	0.0144	0.0	5008	,	,		19465	0.0		0.004	False		,,,				2504	0.0061				p.S397S		Atlas-SNP	.											.	CYP2A7	71	.	0			c.C1191T						PASS	.	G	,	46,4360	48.9+/-83.8	1,44,2158	112.0	98.0	103.0		1191,1038	-3.0	0.6	19	dbSNP_132	103	55,8545	33.8+/-87.4	2,51,4247	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	3,95,6405	AA,AG,GG		0.6395,1.044,0.7766	,	397/495,346/444	41382544	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	1549	exon8			CAGCACGGAGCCC	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1191C>T	19.37:g.41382544G>A		202.0	0.0	0		254.0	119.0	0.468504	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			G|0.992;A|0.008	0.008	strong		0.552	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
PCDHB16	57717	hgsc.bcm.edu	37	5	140564454	140564454	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140564454T>G	ENST00000361016.2	+	1	3475	c.2320T>G	c.(2320-2322)Ttc>Gtc	p.F774V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	774					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TATCCCCAACTTCTCTCCTTA	0.438																																					p.F774V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T2320G						PASS	.						84.0	84.0	84.0					5																	140564454		2203	4300	6503	SO:0001583	missense	57717	exon1			CCCAACTTCTCTC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2320T>G	5.37:g.140564454T>G	ENSP00000354293:p.Phe774Val	133.0	0.0	0		152.0	50.0	0.328947	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	t	10.13	1.265980	0.23136	.	.	ENSG00000196963	ENST00000361016	T	0.50548	0.74	3.79	-0.32	0.12721	.	1.460060	0.04979	N	0.465254	T	0.35970	0.0950	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.22730	-1.0208	10	0.44086	T	0.13	.	4.5606	0.12158	0.147:0.379:0.0:0.4741	.	774	Q9NRJ7	PCDBG_HUMAN	V	774	ENSP00000354293:F774V	ENSP00000354293:F774V	F	+	1	0	PCDHB16	140544638	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-2.526000	0.00947	-0.228000	0.09869	-0.425000	0.05940	TTC	.	.	none		0.438	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:78636484A>C	ENST00000354212.4	-	2	593	c.340T>G	c.(340-342)Tta>Gta	p.L114V	MAGI2_ENST00000419488.1_Missense_Mutation_p.L114V|MAGI2_ENST00000522391.1_Missense_Mutation_p.L114V|MAGI2-AS2_ENST00000411616.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	114	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.L114V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGAAATCGTAAGTTGAGGTAG	0.388																																					p.L114V		Atlas-SNP	.											MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	1	Substitution - Missense(1)	large_intestine(1)	c.T340G						PASS	.						147.0	126.0	133.0					7																	78636484		2203	4300	6503	SO:0001583	missense	9863	exon2			ATCGTAAGTTGAG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.340T>G	7.37:g.78636484A>C	ENSP00000346151:p.Leu114Val	100.0	0.0	0		74.0	25.0	0.337838	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994850	0.74703	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11277	2.89;2.89;2.79	5.29	4.1	0.47936	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	.	.	.	.	T	0.23492	0.0568	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.82	T	0.00647	-1.1628	9	0.35671	T	0.21	.	9.4432	0.38681	0.8477:0.0:0.1523:0.0	.	114;114	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	V	114	ENSP00000405766:L114V;ENSP00000346151:L114V;ENSP00000428389:L114V	ENSP00000346151:L114V	L	-	1	2	MAGI2	78474420	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.746000	0.55127	0.802000	0.34089	0.519000	0.50382	TTA	.	.	none		0.388	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
MBTPS1	8720	hgsc.bcm.edu	37	16	84125394	84125394	+	Silent	SNP	G	G	A	rs113848224	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84125394G>A	ENST00000343411.3	-	7	1401	c.906C>T	c.(904-906)gaC>gaT	p.D302D	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	302	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGTTTAACACGTCGATCTTCT	0.443																																					p.D302D		Atlas-SNP	.											.	MBTPS1	85	.	0			c.C906T						PASS	.	G		0,4400		0,0,2200	103.0	96.0	98.0		906	-6.2	0.1	16	dbSNP_132	98	9,8591	7.1+/-27.0	1,7,4292	yes	coding-synonymous	MBTPS1	NM_003791.2		1,7,6492	AA,AG,GG		0.1047,0.0,0.0692		302/1053	84125394	9,12991	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon7			TAACACGTCGATC	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.906C>T	16.37:g.84125394G>A		120.0	0.0	0		90.0	36.0	0.4	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.998;A|0.002	0.002	strong		0.443	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
FAM83G	644815	hgsc.bcm.edu	37	17	18881605	18881605	+	Missense_Mutation	SNP	C	C	A	rs201344489	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18881605C>A	ENST00000388995.6	-	5	1597	c.1374G>T	c.(1372-1374)caG>caT	p.Q458H	SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.Q458H|FAM83G_ENST00000585154.2_Missense_Mutation_p.Q458H			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	458					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						ACAGCTGGTGCTGGGCGCTGG	0.642													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16140	0.001		0.004	False		,,,				2504	0.002				p.Q458H		Atlas-SNP	.											.	FAM83G	51	.	0			c.G1374T						PASS	.	C	HIS/GLN,,	11,4201		0,11,2095	19.0	24.0	22.0		1374,,	3.6	1.0	17		22	79,8385		0,79,4153	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	24,,	0,90,6248	AA,AC,CC		0.9334,0.2612,0.71	possibly-damaging,,	458/824,,	18881605	90,12586	2106	4232	6338	SO:0001583	missense	644815	exon5			CTGGTGCTGGGCG	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1374G>T	17.37:g.18881605C>A	ENSP00000373647:p.Gln458His	119.0	0.0	0		119.0	72.0	0.605042	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	17.35	3.367567	0.61513	0.002612	0.009334	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.14022	2.54;2.54	5.62	3.62	0.41486	.	1.902850	0.02950	N	0.141633	T	0.27798	0.0684	L	0.56769	1.78	0.26245	N	0.978812	D	0.89917	1.0	D	0.73380	0.98	T	0.02457	-1.1156	10	0.51188	T	0.08	-18.311	8.5714	0.33572	0.0:0.7088:0.0:0.2912	.	458	A6ND36	FA83G_HUMAN	H	458	ENSP00000373647:Q458H;ENSP00000343279:Q458H	ENSP00000343279:Q458H	Q	-	3	2	FAM83G	18822330	0.999000	0.42202	0.997000	0.53966	0.984000	0.73092	0.631000	0.24568	0.732000	0.32470	0.655000	0.94253	CAG	C|0.998;A|0.002	0.002	strong		0.642	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
CACNA2D4	93589	hgsc.bcm.edu	37	12	1910786	1910786	+	Missense_Mutation	SNP	C	C	T	rs62621429	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:1910786C>T	ENST00000382722.5	-	30	3108	c.2746G>A	c.(2746-2748)Gat>Aat	p.D916N	CACNA2D4_ENST00000587995.1_Missense_Mutation_p.D891N|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.D916N|CACNA2D4_ENST00000538027.2_Missense_Mutation_p.D61N|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.D852N|CACNA2D4_ENST00000538450.1_Missense_Mutation_p.D46N|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.D852N	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	916					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		ACAGCACCATCCACCTCCCCC	0.582													C|||	53	0.0105831	0.0015	0.0187	5008	,	,		18810	0.0		0.0308	False		,,,				2504	0.0072				p.D916N	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G2746A						PASS	.	C	ASN/ASP	21,4043		0,21,2011	57.0	59.0	59.0		2746	4.7	1.0	12	dbSNP_129	59	221,8131		0,221,3955	yes	missense	CACNA2D4	NM_172364.4	23	0,242,5966	TT,TC,CC		2.6461,0.5167,1.9491	probably-damaging	916/1138	1910786	242,12174	2032	4176	6208	SO:0001583	missense	93589	exon30			CACCATCCACCTC	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2746G>A	12.37:g.1910786C>T	ENSP00000372169:p.Asp916Asn	49.0	0.0	0		61.0	32.0	0.52459	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	36	0.016483516483516484	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	23	0.030343007915567283	C	17.44	3.391380	0.62066	0.005167	0.026461	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722;ENST00000538450	D;D	0.82711	-1.64;-1.64	5.58	4.69	0.59074	.	0.127286	0.51477	N	0.000100	T	0.71350	0.3329	L	0.58354	1.805	0.80722	D	1	D;D;P	0.55800	0.973;0.96;0.759	P;P;P	0.58928	0.848;0.556;0.521	T	0.77172	-0.2685	10	0.27785	T	0.31	.	11.5041	0.50454	0.0:0.9163:0.0:0.0837	rs62621429	46;916;852	B4DVU4;Q7Z3S7;Q7Z3S7-4	.;CA2D4_HUMAN;.	N	852;916;916;46	ENSP00000372169:D916N;ENSP00000446341:D46N	ENSP00000280663:D916N	D	-	1	0	CACNA2D4	1781047	1.000000	0.71417	0.992000	0.48379	0.977000	0.68977	5.693000	0.68264	1.358000	0.45922	0.655000	0.94253	GAT	C|0.979;T|0.021	0.021	strong		0.582	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
C12orf77	196415	hgsc.bcm.edu	37	12	25148927	25148927	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25148927C>T	ENST00000549828.1	-	3	425	c.221G>A	c.(220-222)aGc>aAc	p.S74N	C12orf77_ENST00000549262.1_Missense_Mutation_p.S19N|C12orf77_ENST00000434912.3_Missense_Mutation_p.S19N	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	74										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						CCATCGTATGCTGTCCAGCGT	0.488																																					p.S74N		Atlas-SNP	.											.	C12orf77	18	.	0			c.G221A						PASS	.						86.0	90.0	88.0					12																	25148927		1985	4159	6144	SO:0001583	missense	196415	exon3			CGTATGCTGTCCA	BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397			27282	protein-coding gene	gene with protein product						12477932	Standard	NM_001101339		Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.221G>A	12.37:g.25148927C>T	ENSP00000447146:p.Ser74Asn	120.0	0.0	0		179.0	42.0	0.234637	NM_001101339		Missense_Mutation	SNP	ENST00000549828.1	37	CCDS44846.1	.	.	.	.	.	.	.	.	.	.	C	3.746	-0.052588	0.07362	.	.	ENSG00000226397	ENST00000549828;ENST00000549262;ENST00000434912	T;T;T	0.55588	0.56;0.51;0.51	2.83	-4.99	0.03010	.	.	.	.	.	T	0.26085	0.0636	N	0.08118	0	0.09310	N	1	B	0.20550	0.046	B	0.12837	0.008	T	0.16867	-1.0388	9	0.87932	D	0	.	5.5379	0.17021	0.1635:0.6411:0.0:0.1954	.	74	C9JDV5	CL097_HUMAN	N	74;19;19	ENSP00000447146:S74N;ENSP00000447028:S19N;ENSP00000403451:S19N	ENSP00000403451:S19N	S	-	2	0	C12orf77	25040194	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.337000	0.00507	-1.357000	0.02180	-0.345000	0.07892	AGC	.	.	none		0.488	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339	
ACAN	176	hgsc.bcm.edu	37	15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	rs533925391		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89402447G>A	ENST00000561243.1	+	11	6631	c.6631G>A	c.(6631-6633)Gtt>Att	p.V2211I	ACAN_ENST00000559004.1_Missense_Mutation_p.V2211I|ACAN_ENST00000352105.7_Missense_Mutation_p.V2211I|ACAN_ENST00000439576.2_Missense_Mutation_p.V2211I			P16112	PGCA_HUMAN	aggrecan	2096	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.|G3.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCAGCTGGGCGTTGTCATCAG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18793	0.0		0.0	False		,,,				2504	0.0				p.V2211I		Atlas-SNP	.											.	ACAN	220	.	0			c.G6631A						PASS	.						44.0	50.0	48.0					15																	89402447		2134	4239	6373	SO:0001583	missense	176	exon12			CTGGGCGTTGTCA	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6631G>A	15.37:g.89402447G>A	ENSP00000453342:p.Val2211Ile	115.0	0.0	0		100.0	47.0	0.47	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	G	0.119	-1.128582	0.01756	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02606	4.36;4.23	5.12	-1.75	0.08031	.	0.642182	0.11888	N	0.519845	T	0.01765	0.0056	N	0.21583	0.68	0.09310	N	1	P;B	0.39311	0.667;0.304	B;B	0.37780	0.258;0.06	T	0.45963	-0.9225	10	0.21540	T	0.41	-2.0E-4	3.0641	0.06209	0.2863:0.11:0.4916:0.1121	.	2211;2211	E7ENV9;E7EX88	.;.	I	2211;2211;2097	ENSP00000387356:V2211I;ENSP00000341615:V2211I	ENSP00000268134:V2097I	V	+	1	0	ACAN	87203451	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.782000	0.04643	-0.274000	0.09232	-1.342000	0.01247	GTT	.	.	none		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
SHC3	53358	hgsc.bcm.edu	37	9	91652977	91652977	+	Silent	SNP	G	G	A	rs56005403	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91652977G>A	ENST00000375835.4	-	11	1893	c.1587C>T	c.(1585-1587)ggC>ggT	p.G529G	SHC3_ENST00000375831.1_Silent_p.G77G|SHC3_ENST00000375830.1_Silent_p.G77G	NM_016848.5	NP_058544.3	Q92529	SHC3_HUMAN	SHC (Src homology 2 domain containing) transforming protein 3	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|insulin receptor signaling pathway (GO:0008286)|learning or memory (GO:0007611)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	signal transducer activity (GO:0004871)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|skin(3)	28						GGACAAAGGAGCCCGGGTTGG	0.632													G|||	19	0.00379393	0.0	0.0029	5008	,	,		16704	0.0		0.0139	False		,,,				2504	0.0031				p.G529G		Atlas-SNP	.											.	SHC3	66	.	0			c.C1587T						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	132.0	134.0	134.0		1587	-0.9	1.0	9	dbSNP_129	134	157,8443	74.8+/-137.4	0,157,4143	no	coding-synonymous	SHC3	NM_016848.5		0,170,6333	AA,AG,GG		1.8256,0.2951,1.3071		529/595	91652977	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	53358	exon11			AAAGGAGCCCGGG	D84361	CCDS6681.1	9q22.1	2013-02-14	2005-05-24		ENSG00000148082	ENSG00000148082		"""SH2 domain containing"""	18181	protein-coding gene	gene with protein product		605263	"""src homology 2 domain containing transforming protein C3"""			8808684	Standard	NM_016848		Approved	N-Shc, NSHC, SHCC	uc004aqf.2	Q92529	OTTHUMG00000020179	ENST00000375835.4:c.1587C>T	9.37:g.91652977G>A		29.0	0.0	0		40.0	20.0	0.5	NM_016848	Q5T7I7|Q8TAP2|Q9UCX5	Silent	SNP	ENST00000375835.4	37	CCDS6681.1																																																																																			G|0.990;A|0.010	0.010	strong		0.632	SHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052986.1	NM_016848	
FABP7	2173	hgsc.bcm.edu	37	6	123104889	123104889	+	Missense_Mutation	SNP	G	G	A	rs77153426	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:123104889G>A	ENST00000368444.3	+	4	696	c.376G>A	c.(376-378)Gtt>Att	p.V126I		NM_001446.3	NP_001437.1	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	126					cell proliferation in forebrain (GO:0021846)|epithelial cell proliferation (GO:0050673)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|prepulse inhibition (GO:0060134)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|Dihomo-gamma-linolenic acid(DB00154)|Icosapent(DB00159)	TGTGGTTGCTGTTCGCCACTA	0.393													G|||	2	0.000399361	0.0	0.0	5008	,	,		15417	0.0		0.001	False		,,,				2504	0.001				p.V126I		Atlas-SNP	.											.	FABP7	10	.	0			c.G376A						PASS	.						175.0	166.0	169.0					6																	123104889		2203	4300	6503	SO:0001583	missense	2173	exon4			GTTGCTGTTCGCC	D88648	CCDS5127.1	6q22-q23	2013-03-01			ENSG00000164434	ENSG00000164434		"""Fatty acid binding protein family"""	3562	protein-coding gene	gene with protein product	"""brain lipid binding protein"""	602965				9375786	Standard	NM_001446		Approved	B-FABP, BLBP	uc003pzf.3	O15540	OTTHUMG00000015489	ENST00000368444.3:c.376G>A	6.37:g.123104889G>A	ENSP00000357429:p.Val126Ile	120.0	0.0	0		137.0	65.0	0.474453	NM_001446	B2R4L1|O14951|Q6IAU7|Q9H047	Missense_Mutation	SNP	ENST00000368444.3	37	CCDS5127.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.128112	0.56721	.	.	ENSG00000164434	ENST00000368444	T	0.08720	3.06	5.4	3.59	0.41128	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.03695	0.0105	L	0.45285	1.41	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.16100	-1.0414	9	0.49607	T	0.09	.	11.852	0.52417	0.143:0.0:0.857:0.0	.	126	O15540	FABP7_HUMAN	I	126	ENSP00000357429:V126I	ENSP00000357429:V126I	V	+	1	0	FABP7	123146588	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.409000	0.59768	1.414000	0.47017	0.462000	0.41574	GTT	.	.	alt		0.393	FABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042037.1	NM_001446	
ACAA1	30	hgsc.bcm.edu	37	3	38167095	38167095	+	Missense_Mutation	SNP	A	A	G	rs2229528	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38167095A>G	ENST00000333167.8	-	11	1332	c.1160T>C	c.(1159-1161)gTc>gCc	p.V387A	Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000450296.1_Missense_Mutation_p.V346A|ACAA1_ENST00000301810.7_Missense_Mutation_p.V294A|ACAA1_ENST00000480865.1_5'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	387			V -> A (in dbSNP:rs2229528). {ECO:0000269|PubMed:15489334}.		alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CAGCGTGATGACCTGTCGTGC	0.612													A|||	60	0.0119808	0.0023	0.0144	5008	,	,		18767	0.0		0.0427	False		,,,				2504	0.0041				p.V387A		Atlas-SNP	.											.	ACAA1	32	.	0			c.T1160C						PASS	.	A	ALA/VAL,ALA/VAL	27,4379	33.5+/-64.1	0,27,2176	66.0	62.0	63.0		881,1160	5.6	1.0	3	dbSNP_131	63	350,8250	118.5+/-177.9	6,338,3956	yes	missense,missense	ACAA1	NM_001130410.1,NM_001607.3	64,64	6,365,6132	GG,GA,AA		4.0698,0.6128,2.8987	benign,benign	294/332,387/425	38167095	377,12629	2203	4300	6503	SO:0001583	missense	30	exon11			GTGATGACCTGTC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.1160T>C	3.37:g.38167095A>G	ENSP00000333664:p.Val387Ala	105.0	0.0	0		100.0	46.0	0.46	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	43|43	0.019688644688644688|0.019688644688644688	3|3	0.006097560975609756|0.006097560975609756	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	A|A	18.59|18.59	3.657401|3.657401	0.67586|0.67586	0.006128|0.006128	0.040698|0.040698	ENSG00000060971|ENSG00000060971	ENST00000452171;ENST00000421218|ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122	.|D;D;D	.|0.83075	.|-1.68;-1.68;-1.68	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	.|0.114891	.|0.64402	.|D	.|0.000015	T|T	0.59183|0.59183	0.2175|0.2175	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.48162	.|0.383;0.906;0.615	.|B;P;P	.|0.50440	.|0.208;0.641;0.544	T|T	0.74705|0.74705	-0.3575|-0.3575	5|10	.|0.49607	.|T	.|0.09	-44.228|-44.228	10.2096|10.2096	0.43132|0.43132	0.926:0.0:0.074:0.0|0.926:0.0:0.074:0.0	rs2229528;rs17845420;rs17858286;rs17845420|rs2229528;rs17845420;rs17858286;rs17845420	.|346;294;387	.|C9JDE9;G5E935;P09110	.|.;.;THIK_HUMAN	P|A	200;277|387;294;346;319	.|ENSP00000333664:V387A;ENSP00000301810:V294A;ENSP00000395183:V346A	.|ENSP00000301810:V294A	S|V	-|-	1|2	0|0	ACAA1|ACAA1	38142099|38142099	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.991000|0.991000	0.79684|0.79684	6.176000|6.176000	0.71955|0.71955	2.144000|2.144000	0.66660|0.66660	0.533000|0.533000	0.62120|0.62120	TCA|GTC	T|0.067;G|0.026	0.026	strong		0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
KIAA1586	57691	hgsc.bcm.edu	37	6	56918304	56918304	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56918304G>A	ENST00000370733.4	+	4	1214	c.1007G>A	c.(1006-1008)tGc>tAc	p.C336Y	KIAA1586_ENST00000545356.1_Missense_Mutation_p.C309Y	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	336							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TATCTCCAGTGCACAATTCAG	0.338																																					p.C336Y		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G1007A						PASS	.						118.0	118.0	118.0					6																	56918304		2203	4298	6501	SO:0001583	missense	57691	exon4			TCCAGTGCACAAT	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.1007G>A	6.37:g.56918304G>A	ENSP00000359768:p.Cys336Tyr	74.0	0.0	0		83.0	31.0	0.373494	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	0.157	-1.085057	0.01888	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.14893	2.47;2.47	2.93	0.941	0.19519	Ribonuclease H-like (1);	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.47275	-0.9130	9	0.02654	T	1	1.9773	3.2772	0.06902	0.1485:0.0:0.5958:0.2557	.	309;336	F5H2N6;Q9HCI6	.;K1586_HUMAN	Y	336;309	ENSP00000359768:C336Y;ENSP00000445507:C309Y	ENSP00000359768:C336Y	C	+	2	0	KIAA1586	57026263	0.107000	0.21998	0.032000	0.17829	0.981000	0.71138	0.017000	0.13399	0.070000	0.16634	0.467000	0.42956	TGC	.	.	none		0.338	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494661G>A	ENST00000237305.7	-	4	360	c.272C>T	c.(271-273)cCt>cTt	p.P91L	SGK1_ENST00000528577.1_Missense_Mutation_p.P119L|SGK1_ENST00000413996.3_Missense_Mutation_p.P105L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.P81L|SGK1_ENST00000475719.2_Missense_Mutation_p.P91L|SGK1_ENST00000367858.5_Missense_Mutation_p.P186L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	91					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.P186L(1)|p.P81L(1)|p.P91L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTTAGCATGAGGATTGGACGA	0.378																																					p.P186L		Atlas-SNP	.											SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C557T						PASS	.						73.0	77.0	76.0					6																	134494661		2203	4300	6503	SO:0001583	missense	6446	exon6			GCATGAGGATTGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.272C>T	6.37:g.134494661G>A	ENSP00000237305:p.Pro91Leu	82.0	0.0	0		81.0	23.0	0.283951	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.349626	0.82132	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.73897	3.3;3.3;3.3;3.3;3.3;-0.79	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.78266	0.4256	M	0.74881	2.28	0.80722	D	1	P;P;P;P;P;P	0.52170	0.89;0.951;0.715;0.739;0.942;0.774	P;P;B;P;P;B	0.49192	0.448;0.495;0.35;0.497;0.602;0.301	T	0.80410	-0.1394	10	0.72032	D	0.01	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	119;105;91;81;186;91	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	L	186;105;91;81;119;91	ENSP00000356832:P186L;ENSP00000396242:P105L;ENSP00000237305:P91L;ENSP00000356831:P81L;ENSP00000434450:P119L;ENSP00000434302:P91L	ENSP00000237305:P91L	P	-	2	0	SGK1	134536354	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	CCT	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
MCMDC2	157777	hgsc.bcm.edu	37	8	67813482	67813482	+	Silent	SNP	G	G	A	rs139959817	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67813482G>A	ENST00000422365.2	+	13	1839	c.1668G>A	c.(1666-1668)ttG>ttA	p.L556L	MCMDC2_ENST00000541540.1_Silent_p.L493L|MCMDC2_ENST00000313616.5_Silent_p.L556L|MCMDC2_ENST00000396592.3_Silent_p.L556L	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	556	MCM.				DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						AATTCAGCTTGGAAGCAGAAA	0.353													G|||	129	0.0257588	0.0038	0.0576	5008	,	,		17119	0.0079		0.0268	False		,,,				2504	0.0501				p.L556L		Atlas-SNP	.											.	MCMDC2	84	.	0			c.G1668A						PASS	.	G	,,	42,4364	45.3+/-79.5	0,42,2161	79.0	79.0	79.0		1668,1668,1668	4.6	1.0	8	dbSNP_134	79	268,8332	102.7+/-163.9	5,258,4037	no	coding-synonymous,coding-synonymous,coding-synonymous	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	,,	5,300,6198	AA,AG,GG		3.1163,0.9532,2.3835	,,	556/633,556/591,556/682	67813482	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	157777	exon13			CAGCTTGGAAGCA	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.1668G>A	8.37:g.67813482G>A		180.0	0.0	0		171.0	65.0	0.380117	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Silent	SNP	ENST00000422365.2	37	CCDS6197.2																																																																																			G|0.979;A|0.021	0.021	strong		0.353	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
KIAA0922	23240	hgsc.bcm.edu	37	4	154519764	154519764	+	Missense_Mutation	SNP	A	A	G	rs72729691	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:154519764A>G	ENST00000409663.3	+	21	2195	c.2143A>G	c.(2143-2145)Atg>Gtg	p.M715V	KIAA0922_ENST00000409959.3_Missense_Mutation_p.M716V|KIAA0922_ENST00000440693.1_Missense_Mutation_p.M632V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	715						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TGTTATTGACATGATTGGCGT	0.408													A|||	21	0.00419329	0.0008	0.0086	5008	,	,		14654	0.0		0.0109	False		,,,				2504	0.0031				p.M716V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A2146G						PASS	.	A	VAL/MET,VAL/MET	10,4396	15.5+/-35.6	0,10,2193	138.0	140.0	139.0		2146,2143	1.9	0.9	4	dbSNP_130	139	71,8529	43.6+/-101.6	0,71,4229	yes	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	21,21	0,81,6422	GG,GA,AA		0.8256,0.227,0.6228	benign,benign	716/1611,715/1610	154519764	81,12925	2203	4300	6503	SO:0001583	missense	23240	exon21			ATTGACATGATTG	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2143A>G	4.37:g.154519764A>G	ENSP00000386574:p.Met715Val	77.0	0.0	0		75.0	34.0	0.453333	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	A	6.379	0.438031	0.12104	0.00227	0.008256	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.16196	2.63;2.36;2.63;2.36	5.79	1.94	0.25998	.	0.199425	0.64402	N	0.000012	T	0.06554	0.0168	L	0.35793	1.09	0.46279	D	0.998961	B;B;B	0.16802	0.019;0.004;0.001	B;B;B	0.22880	0.042;0.006;0.001	T	0.29212	-1.0019	10	0.02654	T	1	-4.0838	5.0559	0.14533	0.5505:0.1489:0.3006:0.0	.	632;716;715	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	V	715;632;716;493	ENSP00000386574:M715V;ENSP00000409663:M632V;ENSP00000386787:M716V;ENSP00000240487:M493V	ENSP00000240487:M493V	M	+	1	0	KIAA0922	154739214	1.000000	0.71417	0.904000	0.35570	0.459000	0.32528	1.972000	0.40540	0.091000	0.17302	0.533000	0.62120	ATG	A|0.994;G|0.006	0.006	strong		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306924	140306924	+	Missense_Mutation	SNP	A	A	T	rs532353795		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140306924A>T	ENST00000253807.2	+	1	447	c.447A>T	c.(445-447)caA>caT	p.Q149H	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.Q149H|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	149	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAATGCCCAAGATGACGACG	0.587																																					p.Q149H		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.A447T						PASS	.						76.0	79.0	78.0					5																	140306924		2203	4300	6503	SO:0001583	missense	56135	exon1			TGCCCAAGATGAC	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.447A>T	5.37:g.140306924A>T	ENSP00000253807:p.Gln149His	95.0	0.0	0		71.0	15.0	0.211268	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.371097	0.24771	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.51325	0.71;0.71	5.7	1.15	0.20763	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.34861	0.0912	L	0.42686	1.345	0.27250	N	0.95892	B;B	0.20164	0.042;0.004	B;B	0.25405	0.06;0.015	T	0.30621	-0.9972	9	0.18710	T	0.47	.	5.7204	0.17985	0.3761:0.0:0.4813:0.1425	.	149;149	Q9H158;Q9H158-2	PCDC1_HUMAN;.	H	149	ENSP00000386356:Q149H;ENSP00000253807:Q149H	ENSP00000253807:Q149H	Q	+	3	2	PCDHAC1	140287108	0.000000	0.05858	0.999000	0.59377	0.965000	0.64279	-2.304000	0.01134	0.110000	0.17919	0.459000	0.35465	CAA	.	.	none		0.587	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
ZFP90	146198	hgsc.bcm.edu	37	16	68598023	68598023	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:68598023A>G	ENST00000570495.1	+	5	1625	c.1333A>G	c.(1333-1335)Acc>Gcc	p.T445A	ZFP90_ENST00000563169.2_Missense_Mutation_p.T445A|ZFP90_ENST00000398253.2_Missense_Mutation_p.T445A			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	445					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		AAGCACTCTTACCGAAGTGAA	0.418																																					p.T445A		Atlas-SNP	.											ZFP90,NS,carcinoma,0,1	ZFP90	67	1	0			c.A1333G						PASS	.						101.0	97.0	98.0					16																	68598023		1996	4184	6180	SO:0001583	missense	146198	exon4			ACTCTTACCGAAG	AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"""Zinc fingers, C2H2-type"", ""-"""	23329	protein-coding gene	gene with protein product		609451	"""zinc finger protein 90 homolog (mouse)"""			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1333A>G	16.37:g.68598023A>G	ENSP00000460547:p.Thr445Ala	79.0	0.0	0		70.0	14.0	0.2	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	A	6.580	0.475358	0.12521	.	.	ENSG00000184939	ENST00000398253	T	0.18810	2.19	5.66	-0.689	0.11313	.	.	.	.	.	T	0.15912	0.0383	L	0.49699	1.58	0.24537	N	0.994082	B	0.06786	0.001	B	0.10450	0.005	T	0.34875	-0.9811	9	0.66056	D	0.02	-3.6822	1.6579	0.02785	0.5267:0.1303:0.2174:0.1255	.	445	Q8TF47	ZFP90_HUMAN	A	445	ENSP00000381304:T445A	ENSP00000381304:T445A	T	+	1	0	ZFP90	67155524	0.000000	0.05858	0.006000	0.13384	0.264000	0.26372	0.966000	0.29331	-0.326000	0.08564	0.533000	0.62120	ACC	.	.	none		0.418	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375	
KRT33A	3883	hgsc.bcm.edu	37	17	39502917	39502917	+	Missense_Mutation	SNP	C	C	A	rs144588166		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39502917C>A	ENST00000007735.3	-	6	924	c.880G>T	c.(880-882)Gac>Tac	p.D294Y		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	294	Coil 2.|Rod.					extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				TCCAGAGAGTCTCGCTGTGGT	0.562													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17962	0.0		0.0	False		,,,				2504	0.0				p.D294Y		Atlas-SNP	.											.	KRT33A	53	.	0			c.G880T						PASS	.	C	TYR/ASP	1,4405	2.1+/-5.4	0,1,2202	48.0	47.0	47.0		880	-1.6	0.8	17	dbSNP_134	47	16,8584	11.9+/-42.8	0,16,4284	yes	missense	KRT33A	NM_004138.2	160	0,17,6486	AA,AC,CC		0.186,0.0227,0.1307	benign	294/405	39502917	17,12989	2203	4300	6503	SO:0001583	missense	3883	exon6			GAGAGTCTCGCTG	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6450	protein-coding gene	gene with protein product	"""hard keratin type I 3I"""	602761	"""keratin, hair, acidic, 3A"""	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.880G>T	17.37:g.39502917C>A	ENSP00000007735:p.Asp294Tyr	92.0	0.0	0		73.0	30.0	0.410959	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	37	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	C	6.070	0.381145	0.11466	2.27E-4	0.00186	ENSG00000006059	ENST00000007735	D	0.89552	-2.53	4.55	-1.56	0.08532	Filament (1);	0.271361	0.32671	N	0.005792	D	0.87853	0.6282	M	0.85197	2.74	0.20196	N	0.999928	B	0.12630	0.006	B	0.23852	0.049	T	0.80407	-0.1395	10	0.59425	D	0.04	.	9.8523	0.41064	0.0:0.6084:0.0:0.3916	.	294	O76009	KT33A_HUMAN	Y	294	ENSP00000007735:D294Y	ENSP00000007735:D294Y	D	-	1	0	KRT33A	36756443	0.000000	0.05858	0.756000	0.31282	0.062000	0.15995	-0.572000	0.05881	-0.282000	0.09128	-0.302000	0.09304	GAC	C|0.999;A|0.001	0.001	strong		0.562	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138	
CYP2B6	1555	hgsc.bcm.edu	37	19	41497346	41497346	+	Missense_Mutation	SNP	A	A	G	rs35303484	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41497346A>G	ENST00000324071.4	+	1	143	c.136A>G	c.(136-138)Atg>Gtg	p.M46V	CYP2B6_ENST00000598834.1_3'UTR	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	46			M -> V (in allele CYP2B6*11; dbSNP:rs35303484). {ECO:0000269|PubMed:15190123}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	CCTTCTGCAGATGGATAGAAG	0.567													A|||	6	0.00119808	0.0008	0.0	5008	,	,		18573	0.0		0.004	False		,,,				2504	0.001				p.M46V		Atlas-SNP	.											.	CYP2B6	79	.	0			c.A136G	GRCh37	CM042692	CYP2B6	M	rs35303484	PASS	.	A	VAL/MET	5,4401	9.9+/-24.2	0,5,2198	147.0	165.0	159.0		136	0.6	0.8	19	dbSNP_126	159	32,8568	22.2+/-67.0	0,32,4268	no	missense	CYP2B6	NM_000767.4	21	0,37,6466	GG,GA,AA		0.3721,0.1135,0.2845	benign	46/492	41497346	37,12969	2203	4300	6503	SO:0001583	missense	1555	exon1			CTGCAGATGGATA	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.136A>G	19.37:g.41497346A>G	ENSP00000324648:p.Met46Val	28.0	0.0	0		32.0	16.0	0.5	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	7.340	0.620661	0.14193	0.001135	0.003721	ENSG00000197408	ENST00000324071	T	0.01228	5.14	3.1	0.644	0.17776	.	0.174316	0.40064	U	0.001199	T	0.01061	0.0035	N	0.17901	0.54	0.40857	D	0.983801	P	0.40431	0.717	B	0.38106	0.265	T	0.71886	-0.4457	10	0.35671	T	0.21	.	6.9443	0.24510	0.5213:0.4787:0.0:0.0	rs35303484	46	P20813	CP2B6_HUMAN	V	46	ENSP00000324648:M46V	ENSP00000324648:M46V	M	+	1	0	CYP2B6	46189186	1.000000	0.71417	0.845000	0.33349	0.095000	0.18619	0.538000	0.23160	0.388000	0.25054	-1.020000	0.02445	ATG	A|0.997;G|0.003;T|0.000	0.003	strong		0.567	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
GMPS	8833	hgsc.bcm.edu	37	3	155633817	155633817	+	Nonsense_Mutation	SNP	G	G	T	rs201869567		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:155633817G>T	ENST00000496455.2	+	9	1383	c.1048G>T	c.(1048-1050)Gaa>Taa	p.E350*	GMPS_ENST00000295920.7_Nonsense_Mutation_p.E251*	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	350	GMPS ATP-PPase. {ECO:0000255|PROSITE- ProRule:PRU00886}.				glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	GATTGCCAATGAAGTAATTGG	0.368			T	MLL	AML																																p.E350X	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.G1048T						PASS	.						66.0	61.0	62.0					3																	155633817		1824	4087	5911	SO:0001587	stop_gained	8833	exon9			GCCAATGAAGTAA	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"""GMP synthase"""	600358	"""guanine monphosphate synthetase"""			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1048G>T	3.37:g.155633817G>T	ENSP00000419851:p.Glu350*	70.0	0.0	0		53.0	4.0	0.0754717	NM_003875	A8K639|B4DXV7|F8W720	Nonsense_Mutation	SNP	ENST00000496455.2	37	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	G	40	8.493974	0.98836	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.36	5.36	0.76844	.	0.261311	0.38605	N	0.001621	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-21.8965	19.0809	0.93180	0.0:0.0:1.0:0.0	.	.	.	.	X	350;251;299;350	.	ENSP00000295920:E251X	E	+	1	0	GMPS	157116511	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.149000	0.94659	2.505000	0.84491	0.549000	0.68633	GAA	G|0.999;A|0.001	.	alt		0.368	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2		
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	rs572028879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:96810609C>T	ENST00000288943.4	-	2	486	c.401G>A	c.(400-402)gGc>gAc	p.G134D	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	134	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GCCCTGGAAGCCGTCGAAGCC	0.697													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11195	0.0		0.0	False		,,,				2504	0.0				p.G134D		Atlas-SNP	.											.	DUSP2	20	.	0			c.G401A						PASS	.						15.0	20.0	18.0					2																	96810609		2094	4175	6269	SO:0001583	missense	1844	exon2			TGGAAGCCGTCGA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.401G>A	2.37:g.96810609C>T	ENSP00000288943:p.Gly134Asp	75.0	0.0	0		60.0	20.0	0.333333	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	C	3.560	-0.089892	0.07053	.	.	ENSG00000158050	ENST00000288943	T	0.26373	1.74	4.31	2.38	0.29361	Rhodanese-like (5);	0.285507	0.32736	N	0.005712	T	0.26774	0.0655	L	0.58101	1.795	0.25586	N	0.986743	B	0.31459	0.324	B	0.37091	0.241	T	0.14504	-1.0470	10	0.28530	T	0.3	.	10.6808	0.45813	0.0:0.5226:0.4774:0.0	.	134	Q05923	DUS2_HUMAN	D	134	ENSP00000288943:G134D	ENSP00000288943:G134D	G	-	2	0	DUSP2	96174336	0.037000	0.19845	0.471000	0.27229	0.207000	0.24258	0.181000	0.16880	0.349000	0.23975	0.456000	0.33151	GGC	.	.	none		0.697	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
CREB3L4	148327	hgsc.bcm.edu	37	1	153941842	153941842	+	Missense_Mutation	SNP	T	T	G	rs186432230		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153941842T>G	ENST00000368607.3	+	4	720	c.454T>G	c.(454-456)Tcc>Gcc	p.S152A	CREB3L4_ENST00000368603.1_Missense_Mutation_p.S152A|CREB3L4_ENST00000271889.4_Missense_Mutation_p.S152A|CREB3L4_ENST00000405694.3_Missense_Mutation_p.S5A|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000368600.3_Missense_Mutation_p.S132A|CREB3L4_ENST00000368601.1_Missense_Mutation_p.S152A|RP11-422P24.10_ENST00000608147.1_RNA	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	152					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGTGCCTGATTCCTGCATGGT	0.577													T|||	1	0.000199681	0.0	0.0	5008	,	,		21087	0.0		0.001	False		,,,				2504	0.0				p.S152A		Atlas-SNP	.											.	CREB3L4	36	.	0			c.T454G						PASS	.						134.0	122.0	126.0					1																	153941842		2203	4300	6503	SO:0001583	missense	148327	exon4			CCTGATTCCTGCA	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"""basic leucine zipper proteins"""	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.454T>G	1.37:g.153941842T>G	ENSP00000357596:p.Ser152Ala	125.0	0.0	0		119.0	62.0	0.521008	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	37	CCDS1056.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	1.414	-0.574595	0.03882	.	.	ENSG00000143578	ENST00000405694;ENST00000449724;ENST00000368607;ENST00000271889;ENST00000368601;ENST00000368603;ENST00000368600;ENST00000431292	T;T;T;T;T;T;T;T	0.74106	-0.81;-0.05;-0.04;-0.04;1.02;-0.04;-0.04;1.0	4.64	1.64	0.23874	.	0.952104	0.08771	N	0.896201	T	0.13841	0.0335	N	0.01209	-0.955	0.23406	N	0.997746	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32322	-0.9911	10	0.02654	T	1	.	3.111	0.06359	0.0976:0.1705:0.5475:0.1844	.	132;152	Q5T4L0;Q8TEY5	.;CR3L4_HUMAN	A	5;132;152;152;152;152;132;152	ENSP00000385104:S5A;ENSP00000391847:S132A;ENSP00000357596:S152A;ENSP00000271889:S152A;ENSP00000357590:S152A;ENSP00000357592:S152A;ENSP00000357589:S132A;ENSP00000402308:S152A	ENSP00000271889:S152A	S	+	1	0	CREB3L4	152208466	0.269000	0.24143	0.782000	0.31804	0.760000	0.43138	0.381000	0.20619	0.179000	0.19938	-0.302000	0.09304	TCC	T|1.000;G|0.000	0.000	strong		0.577	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898	
OR9Q1	219956	hgsc.bcm.edu	37	11	57947163	57947163	+	Missense_Mutation	SNP	G	G	A	rs111629598	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57947163G>A	ENST00000335397.3	+	3	563	c.247G>A	c.(247-249)Gca>Aca	p.A83T		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, member 1	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Breast(21;0.222)				CCAGATGCTGGCAGTGCTGCT	0.522													G|||	71	0.0141773	0.0015	0.0216	5008	,	,		22598	0.0		0.0348	False		,,,				2504	0.0194				p.A83T		Atlas-SNP	.											.	OR9Q1	60	.	0			c.G247A						PASS	.	G	THR/ALA	28,4374	34.3+/-65.2	0,28,2173	163.0	139.0	148.0		247	4.8	0.8	11	dbSNP_132	148	282,8310	106.2+/-167.1	10,262,4024	yes	missense	OR9Q1	NM_001005212.3	58	10,290,6197	AA,AG,GG		3.2821,0.6361,2.3857	possibly-damaging	83/311	57947163	310,12684	2201	4296	6497	SO:0001583	missense	219956	exon3			ATGCTGGCAGTGC	AB065734	CCDS31543.1	11q12.1	2012-08-09				ENSG00000186509		"""GPCR / Class A : Olfactory receptors"""	14724	protein-coding gene	gene with protein product							Standard	NM_001005212		Approved		uc001nmj.3	Q8NGQ5		ENST00000335397.3:c.247G>A	11.37:g.57947163G>A	ENSP00000334934:p.Ala83Thr	175.0	0.0	0		210.0	105.0	0.5	NM_001005212	Q2TAN3|Q96RA7	Missense_Mutation	SNP	ENST00000335397.3	37	CCDS31543.1	41	0.018772893772893772	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	8.610	0.888822	0.17540	0.006361	0.032821	ENSG00000186509	ENST00000335397	T	0.00397	7.57	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	0.435428	0.19416	N	0.114802	T	0.00073	0.0002	L	0.37800	1.135	0.22968	N	0.998493	P	0.44627	0.839	B	0.33750	0.169	T	0.64394	-0.6418	10	0.41790	T	0.15	-8.0467	13.2507	0.60050	0.0:0.1593:0.8407:0.0	.	83	Q8NGQ5	OR9Q1_HUMAN	T	83	ENSP00000334934:A83T	ENSP00000334934:A83T	A	+	1	0	OR9Q1	57703739	0.014000	0.17966	0.758000	0.31321	0.089000	0.18198	0.459000	0.21908	2.680000	0.91292	0.563000	0.77884	GCA	G|0.976;A|0.024	0.024	strong		0.522	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Silent	SNP	A	A	C	rs115653109	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:23230404A>C	ENST00000526893.1	+	1	445	c.171A>C	c.(169-171)ggA>ggC	p.G57G	IGLL5_ENST00000531372.1_Silent_p.G57G|IGLL5_ENST00000532223.2_Silent_p.G57G|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTCAGTTGGAAGCAGCCGAT	0.662																																					p.E22A		Atlas-SNP	.											.	IGLL5	26	.	0			c.A65C						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			AGTTGGAAGCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.171A>C	22.37:g.23230404A>C		141.0	0.0	0		41.0	12.0	0.292683	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			A|0.999;G|0.001	.	alt		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
LAMA1	284217	hgsc.bcm.edu	37	18	6950847	6950847	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:6950847A>C	ENST00000389658.3	-	58	8424	c.8331T>G	c.(8329-8331)ttT>ttG	p.F2777L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2777	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGCCAAGGTCAAACATGAAGT	0.572																																					p.F2777L		Atlas-SNP	.											.	LAMA1	458	.	0			c.T8331G						PASS	.						117.0	100.0	105.0					18																	6950847		2203	4300	6503	SO:0001583	missense	284217	exon58			AAGGTCAAACATG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8331T>G	18.37:g.6950847A>C	ENSP00000374309:p.Phe2777Leu	110.0	0.0	0		103.0	27.0	0.262136	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.017652	0.35606	.	.	ENSG00000101680	ENST00000389658	T	0.73575	-0.76	5.5	0.425	0.16473	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.200169	0.45126	D	0.000391	T	0.60130	0.2245	L	0.39514	1.22	0.37392	D	0.9125	B;B	0.28350	0.083;0.208	B;B	0.33690	0.028;0.168	T	0.45512	-0.9256	10	0.20519	T	0.43	.	5.6623	0.17676	0.5896:0.1311:0.2793:0.0	.	2777;107	P25391;B3KSD8	LAMA1_HUMAN;.	L	2777	ENSP00000374309:F2777L	ENSP00000374309:F2777L	F	-	3	2	LAMA1	6940847	1.000000	0.71417	0.995000	0.50966	0.400000	0.30750	2.104000	0.41815	-0.144000	0.11314	-0.441000	0.05720	TTT	.	.	none		0.572	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
KIAA1804	84451	hgsc.bcm.edu	37	1	233511675	233511675	+	Missense_Mutation	SNP	A	A	C	rs35758282	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233511675A>C	ENST00000366624.3	+	7	1950	c.1689A>C	c.(1687-1689)gaA>gaC	p.E563D	MLK4_ENST00000366622.1_Missense_Mutation_p.E9D	NM_032435.2	NP_115811.2																					CTTCAGATGAAAGCAATAAAA	0.308													A|||	8	0.00159744	0.0	0.0029	5008	,	,		17798	0.0		0.006	False		,,,				2504	0.0				p.E563D		Atlas-SNP	.											.	KIAA1804	129	.	0			c.A1689C						PASS	.	A	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	82.0	84.0	84.0		1689	-0.7	1.0	1	dbSNP_126	84	21,8577	16.0+/-53.3	0,21,4278	yes	missense	KIAA1804	NM_032435.2	45	0,22,6480	CC,CA,AA		0.2442,0.0227,0.1692	benign	563/1037	233511675	22,12982	2203	4299	6502	SO:0001583	missense	0	exon7			AGATGAAAGCAAT																												ENST00000366624.3:c.1689A>C	1.37:g.233511675A>C	ENSP00000355583:p.Glu563Asp	112.0	0.0	0		116.0	53.0	0.456897	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	12.19	1.862541	0.32884	2.27E-4	0.002442	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.10960	2.82;2.82	5.44	-0.691	0.11305	.	0.000000	0.85682	D	0.000000	T	0.10121	0.0248	L	0.31476	0.935	0.36608	D	0.875022	D;B	0.56521	0.976;0.191	D;B	0.62955	0.909;0.084	T	0.08848	-1.0702	10	0.87932	D	0	.	6.7874	0.23682	0.4566:0.0:0.4213:0.1221	rs35758282	10;563	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	D	563;9	ENSP00000355583:E563D;ENSP00000355581:E9D	ENSP00000355581:E9D	E	+	3	2	RP5-862P8.2	231578298	0.799000	0.28903	0.998000	0.56505	0.984000	0.73092	0.024000	0.13555	-0.026000	0.13895	0.533000	0.62120	GAA	A|0.998;C|0.002	0.002	strong		0.308	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
TAS2R14	50840	hgsc.bcm.edu	37	12	11091206	11091206	+	Missense_Mutation	SNP	G	G	A	rs35804287	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11091206G>A	ENST00000537503.1	-	1	656	c.601C>T	c.(601-603)Ctc>Ttc	p.L201F	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	201			L -> F (in dbSNP:rs35804287).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						GAGAAGATGAGGAGAAGAAAC	0.418													G|||	30	0.00599042	0.0	0.0043	5008	,	,		19120	0.0		0.0249	False		,,,				2504	0.002				p.L201F		Atlas-SNP	.											.	TAS2R14	26	.	0			c.C601T						PASS	.	G	PHE/LEU	19,4387	26.2+/-53.5	0,19,2184	86.0	90.0	89.0		601	-0.2	0.0	12	dbSNP_126	89	157,8443	74.8+/-137.4	4,149,4147	yes	missense	TAS2R14	NM_023922.1	22	4,168,6331	AA,AG,GG		1.8256,0.4312,1.3532	probably-damaging	201/318	11091206	176,12830	2203	4300	6503	SO:0001583	missense	50840	exon1			AGATGAGGAGAAG	AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.601C>T	12.37:g.11091206G>A	ENSP00000441949:p.Leu201Phe	78.0	0.0	0		77.0	42.0	0.545455	NM_023922	Q645X3	Missense_Mutation	SNP	ENST00000537503.1	37	CCDS8637.1	29	0.013278388278388278	0	0.0	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	13.65	2.301826	0.40694	0.004312	0.018256	ENSG00000212127	ENST00000537503	T	0.03272	3.99	3.95	-0.176	0.13311	.	0.112267	0.33534	U	0.004812	T	0.04318	0.0119	M	0.85945	2.785	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.06215	-1.0839	10	0.87932	D	0	.	3.3203	0.07048	0.316:0.0:0.5031:0.1809	rs35804287	201	Q9NYV8	T2R14_HUMAN	F	201	ENSP00000441949:L201F	ENSP00000375094:L201F	L	-	1	0	TAS2R14	10982473	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-1.779000	0.01777	-0.144000	0.11314	-0.241000	0.12123	CTC	G|0.989;A|0.011	0.011	strong		0.418	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922	
SPDEF	25803	hgsc.bcm.edu	37	6	34507305	34507305	+	Silent	SNP	C	C	T	rs374584207		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34507305C>T	ENST00000374037.3	-	4	1083	c.669G>A	c.(667-669)gcG>gcA	p.A223A	SPDEF_ENST00000544425.1_Intron	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	223					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						AGTAGTGAATCGCCCCAGGTG	0.687																																					p.A223A		Atlas-SNP	.											.	SPDEF	34	.	0			c.G669A						PASS	.	C		0,4328		0,0,2164	10.0	11.0	11.0		669	-10.4	0.0	6		11	4,8518		0,4,4257	no	coding-synonymous	SPDEF	NM_012391.1		0,4,6421	TT,TC,CC		0.0469,0.0,0.0311		223/336	34507305	4,12846	2164	4261	6425	SO:0001819	synonymous_variant	25803	exon4			GTGAATCGCCCCA	AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"""SAM pointed domain containing ets transcription factor"""			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.669G>A	6.37:g.34507305C>T		217.0	0.0	0		190.0	34.0	0.178947	NM_012391	B4DWH8|F5H778	Silent	SNP	ENST00000374037.3	37	CCDS4794.1																																																																																			.	.	weak		0.687	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705754	68705754	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68705754G>A	ENST00000255078.3	+	14	2827	c.2716G>A	c.(2716-2718)Gtc>Atc	p.V906I		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	906					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CACAGCCGGCGTCACAACCCT	0.637																																					p.V906I		Atlas-SNP	.											IGHMBP2,right_upper_lobe,carcinoma,0,1	IGHMBP2	83	1	0			c.G2716A						PASS	.						42.0	40.0	41.0					11																	68705754		2200	4294	6494	SO:0001583	missense	3508	exon14			GCCGGCGTCACAA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2716G>A	11.37:g.68705754G>A	ENSP00000255078:p.Val906Ile	65.0	0.0	0		50.0	6.0	0.12	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.456863	0.43634	.	.	ENSG00000132740	ENST00000255078	T	0.42131	0.98	5.0	1.51	0.23008	Zinc finger, AN1-type (4);	0.649507	0.15581	N	0.254934	T	0.41789	0.1174	M	0.63428	1.95	0.80722	D	1	D	0.61080	0.989	P	0.46237	0.508	T	0.34925	-0.9809	10	0.59425	D	0.04	-11.9797	7.9942	0.30258	0.3319:0.0:0.6681:0.0	.	906	P38935	SMBP2_HUMAN	I	906	ENSP00000255078:V906I	ENSP00000255078:V906I	V	+	1	0	IGHMBP2	68462330	1.000000	0.71417	0.163000	0.22734	0.003000	0.03518	4.239000	0.58694	0.293000	0.22520	0.462000	0.41574	GTC	.	.	none		0.637	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
APOLD1	81575	hgsc.bcm.edu	37	12	12940402	12940402	+	Missense_Mutation	SNP	C	C	T	rs146348815		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12940402C>T	ENST00000326765.6	+	2	726	c.656C>T	c.(655-657)aCc>aTc	p.T219I	APOLD1_ENST00000356591.4_Missense_Mutation_p.T188I	NM_001130415.1	NP_001123887.1	Q96LR9	APLD1_HUMAN	apolipoprotein L domain containing 1	219					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|endothelial cell activation (GO:0042118)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|regulation of endothelial cell differentiation (GO:0045601)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	5		Prostate(47;0.0632)		BRCA - Breast invasive adenocarcinoma(232;0.0338)|GBM - Glioblastoma multiforme(207;0.149)		GAGGGGGACACCAAGGTTAGC	0.612																																					p.T219I		Atlas-SNP	.											.	APOLD1	10	.	0			c.C656T						PASS	.	C	ILE/THR,ILE/THR	0,4406		0,0,2203	63.0	72.0	69.0		656,563	3.4	1.0	12	dbSNP_134	69	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	APOLD1	NM_001130415.1,NM_030817.2	89,89	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	219/280,188/249	12940402	2,13004	2203	4300	6503	SO:0001583	missense	81575	exon2			GGGACACCAAGGT	AL136783	CCDS8654.1, CCDS44833.1	12p13.2	2006-02-03	2006-01-23		ENSG00000178878	ENSG00000178878			25268	protein-coding gene	gene with protein product		612456				11230166	Standard	NM_030817		Approved	FLJ25138, DKFZP434F0318	uc001rau.4	Q96LR9	OTTHUMG00000153561	ENST00000326765.6:c.656C>T	12.37:g.12940402C>T	ENSP00000324277:p.Thr219Ile	87.0	0.0	0		80.0	30.0	0.375	NM_001130415	Q8IVR2|Q9H0I5	Missense_Mutation	SNP	ENST00000326765.6	37	CCDS44833.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.913823	0.52439	0.0	2.33E-4	ENSG00000178878	ENST00000326765;ENST00000356591	T;T	0.01379	4.96;4.96	5.35	3.43	0.39272	.	0.204155	0.35378	U	0.003241	T	0.01800	0.0057	L	0.32530	0.975	0.34187	D	0.67166	B;B	0.28055	0.199;0.199	B;B	0.24006	0.031;0.05	T	0.39981	-0.9587	10	0.87932	D	0	-15.4625	15.3834	0.74679	0.0:0.735:0.265:0.0	.	188;219	A0AVN6;Q96LR9	.;APLD1_HUMAN	I	219;188	ENSP00000324277:T219I;ENSP00000348998:T188I	ENSP00000324277:T219I	T	+	2	0	APOLD1	12831669	0.988000	0.35896	0.997000	0.53966	0.271000	0.26615	1.560000	0.36331	0.575000	0.29434	0.579000	0.79373	ACC	C|1.000;T|0.000	0.000	weak		0.612	APOLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331627.1	NM_030817	
KLHL42	57542	hgsc.bcm.edu	37	12	27950775	27950775	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27950775G>A	ENST00000381271.2	+	3	1505	c.1194G>A	c.(1192-1194)ggG>ggA	p.G398G	RP11-860B13.3_ENST00000543527.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	398					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											TCGTGGGGGGGTGTCTCCACG	0.597																																					p.G398G		Atlas-SNP	.											.	.	.	.	0			c.G1194A						PASS	.						101.0	97.0	99.0					12																	27950775		2203	4300	6503	SO:0001819	synonymous_variant	57542	exon3			GGGGGGGTGTCTC	AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"""Kelch-like"""	29252	protein-coding gene	gene with protein product			"""kelch domain containing 5"""	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.1194G>A	12.37:g.27950775G>A		60.0	0.0	0		52.0	17.0	0.326923	NM_020782	Q2VPK1|Q8N334	Silent	SNP	ENST00000381271.2	37	CCDS31763.1																																																																																			.	.	none		0.597	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782	
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775367	27775367	+	Silent	SNP	C	C	T	rs563781327		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27775367C>T	ENST00000377401.2	-	1	342	c.318G>A	c.(316-318)gaG>gaA	p.E106E	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	106					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						GCTTGGCCAGCTCCCCCGGAA	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17875	0.0		0.0	False		,,,				2504	0.0				p.E106E		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.G318A						PASS	.						74.0	77.0	76.0					6																	27775367		2203	4300	6503	SO:0001819	synonymous_variant	8340	exon1			GGCCAGCTCCCCC	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"""Histones / Replication-dependent"""	4748	protein-coding gene	gene with protein product		602800	"""H2B histone family, member C"", ""histone 1, H2bl"""	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.318G>A	6.37:g.27775367C>T		115.0	0.0	0		94.0	29.0	0.308511	NM_003519	B2R5A3|Q52LW9	Silent	SNP	ENST00000377401.2	37	CCDS4625.1																																																																																			.	.	none		0.612	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519	
MDGA1	266727	hgsc.bcm.edu	37	6	37605158	37605158	+	Missense_Mutation	SNP	C	C	T	rs201115181	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:37605158C>T	ENST00000434837.3	-	17	4032	c.2854G>A	c.(2854-2856)Gcg>Acg	p.A952T	MDGA1_ENST00000297153.7_Missense_Mutation_p.A956T	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	952					brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CTCTGCAACGCCAAGAGGAAG	0.632													C|||	4	0.000798722	0.0008	0.0029	5008	,	,		18342	0.0		0.001	False		,,,				2504	0.0				p.A952T		Atlas-SNP	.											MDGA1,NS,carcinoma,+2,1	MDGA1	104	1	0			c.G2854A						PASS	.	C	THR/ALA	1,4071		0,1,2035	41.0	46.0	45.0		2854	3.8	1.0	6		45	12,8338		0,12,4163	yes	missense	MDGA1	NM_153487.3	58	0,13,6198	TT,TC,CC		0.1437,0.0246,0.1047	benign	952/956	37605158	13,12409	2036	4175	6211	SO:0001583	missense	266727	exon17			GCAACGCCAAGAG	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2854G>A	6.37:g.37605158C>T	ENSP00000402584:p.Ala952Thr	127.0	0.0	0		101.0	20.0	0.19802	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	17.24	3.339139	0.60963	2.46E-4	0.001437	ENSG00000112139	ENST00000434837;ENST00000297153	T;T	0.55588	0.51;0.65	4.77	3.83	0.44106	.	22.481800	0.00424	N	0.000065	T	0.18002	0.0432	N	0.08118	0	0.24923	N	0.991966	B	0.34103	0.437	B	0.24541	0.054	T	0.11275	-1.0594	10	0.62326	D	0.03	.	11.7524	0.51855	0.1766:0.8233:0.0:0.0	.	952	Q8NFP4	MDGA1_HUMAN	T	952;956	ENSP00000402584:A952T;ENSP00000297153:A956T	ENSP00000297153:A956T	A	-	1	0	MDGA1	37713136	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	3.082000	0.50128	2.353000	0.79882	0.555000	0.69702	GCG	C|0.999;T|0.001	0.001	strong		0.632	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
ZNF831	128611	hgsc.bcm.edu	37	20	57768655	57768655	+	Missense_Mutation	SNP	G	G	A	rs61743779	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:57768655G>A	ENST00000371030.2	+	1	2581	c.2581G>A	c.(2581-2583)Gat>Aat	p.D861N		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	861							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCAGGATGCCGATCCCGGGGA	0.652													.|||	19	0.00379393	0.0106	0.0	5008	,	,		13970	0.0		0.004	False		,,,				2504	0.001				p.D861N		Atlas-SNP	.											.	ZNF831	287	.	0			c.G2581A						PASS	.	G	ASN/ASP	37,3899		0,37,1931	32.0	39.0	37.0		2581	4.0	0.0	20	dbSNP_129	37	78,8218		0,78,4070	yes	missense	ZNF831	NM_178457.1	23	0,115,6001	AA,AG,GG		0.9402,0.94,0.9402	possibly-damaging	861/1678	57768655	115,12117	1968	4148	6116	SO:0001583	missense	128611	exon1			GATGCCGATCCCG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2581G>A	20.37:g.57768655G>A	ENSP00000360069:p.Asp861Asn	61.0	0.0	0		53.0	30.0	0.566038	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	9	0.004120879120879121	5	0.01016260162601626	0	0.0	0	0.0	4	0.005277044854881266	G	14.30	2.493208	0.44352	0.0094	0.009402	ENSG00000124203	ENST00000371030	T	0.06687	3.27	4.91	3.95	0.45737	.	1.458410	0.04186	N	0.327383	T	0.07818	0.0196	L	0.27053	0.805	0.09310	N	1	D	0.58268	0.982	P	0.47102	0.537	T	0.34378	-0.9831	10	0.51188	T	0.08	-1.9265	9.8204	0.40878	0.0972:0.0:0.9028:0.0	rs61743779	861	Q5JPB2	ZN831_HUMAN	N	861	ENSP00000360069:D861N	ENSP00000360069:D861N	D	+	1	0	ZNF831	57202050	0.000000	0.05858	0.015000	0.15790	0.009000	0.06853	-0.138000	0.10374	1.186000	0.42985	0.655000	0.94253	GAT	G|0.996;A|0.004	0.004	strong		0.652	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
TIGD2	166815	hgsc.bcm.edu	37	4	90034450	90034450	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:90034450T>C	ENST00000317005.2	+	1	483	c.325T>C	c.(325-327)Ttt>Ctt	p.F109L	FAM13A_ENST00000502459.1_5'Flank|RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	109	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		AGCCAAGTTCTTTTTTGATGC	0.433																																					p.F109L		Atlas-SNP	.											.	TIGD2	36	.	0			c.T325C						PASS	.						116.0	116.0	116.0					4																	90034450		2201	4298	6499	SO:0001583	missense	166815	exon1			AAGTTCTTTTTTG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.325T>C	4.37:g.90034450T>C	ENSP00000317170:p.Phe109Leu	63.0	0.0	0		76.0	7.0	0.0921053	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	t	15.10	2.732150	0.48939	.	.	ENSG00000180346	ENST00000317005	T	0.20598	2.06	4.02	4.02	0.46733	Homeodomain-related (1);Pogo transposase / Cenp-B / PDC2, DNA-binding HTH domain (3);Homeodomain-like (1);	0.000000	0.42172	U	0.000748	T	0.12732	0.0309	N	0.11892	0.195	0.35836	D	0.825657	B	0.30326	0.276	B	0.37833	0.259	T	0.20438	-1.0275	10	0.10636	T	0.68	-5.0561	10.9959	0.47575	0.0:0.0:0.0:1.0	.	109	Q4W5G0	TIGD2_HUMAN	L	109	ENSP00000317170:F109L	ENSP00000317170:F109L	F	+	1	0	TIGD2	90253473	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.865000	0.39479	1.703000	0.51240	0.446000	0.29264	TTT	.	.	none		0.433	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715	
ATM	472	hgsc.bcm.edu	37	11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	rs4986761	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108124761T>C	ENST00000452508.2	+	14	2308	c.2119T>C	c.(2119-2121)Tct>Cct	p.S707P	ATM_ENST00000278616.4_Missense_Mutation_p.S707P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	707			S -> P (in dbSNP:rs4986761). {ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846}.|YSS -> FIP (in AT; might be associated with susceptibility to cancer).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.S707P(2)|p.S707fs*29(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TAATTACTCATCTGAGGTGAG	0.393			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			T|||	22	0.00439297	0.0	0.0101	5008	,	,		16199	0.0		0.0129	False		,,,				2504	0.002				p.S707P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM,NS,carcinoma,0,2	ATM	1657	2	3	Substitution - Missense(2)|Deletion - Frameshift(1)	breast(2)|haematopoietic_and_lymphoid_tissue(1)	c.T2119C	GRCh37	CM013692	ATM	M	rs4986761	PASS	.	T	PRO/SER	17,4383	21.2+/-45.6	0,17,2183	55.0	55.0	55.0		2119	3.8	1.0	11	dbSNP_111	55	94,8502	50.6+/-110.7	1,92,4205	yes	missense	ATM	NM_000051.3	74	1,109,6388	CC,CT,TT		1.0935,0.3864,0.8541	benign	707/3057	108124761	111,12885	2200	4298	6498	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	TACTCATCTGAGG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2119T>C	11.37:g.108124761T>C	ENSP00000388058:p.Ser707Pro	53.0	0.0	0		41.0	32.0	0.780488	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	11.63	1.694897	0.30052	0.003864	0.010935	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.78364	-1.17;-1.17;-1.17	6.11	3.81	0.43845	Armadillo-type fold (1);	0.179298	0.50627	N	0.000119	T	0.52141	0.1716	N	0.17872	0.535	0.23076	N	0.998335	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	10	0.31617	T	0.26	.	7.5463	0.27768	0.0:0.2362:0.0:0.7638	rs4986761;rs52832782;rs4986761	707	Q13315	ATM_HUMAN	P	707	ENSP00000435747:S707P;ENSP00000278616:S707P;ENSP00000388058:S707P	ENSP00000278616:S707P	S	+	1	0	ATM	107629971	0.015000	0.18098	0.999000	0.59377	0.911000	0.54048	-0.127000	0.10547	0.553000	0.29044	0.533000	0.62120	TCT	T|0.993;C|0.007	0.007	strong		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
VGLL2	245806	hgsc.bcm.edu	37	6	117586990	117586990	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:117586990T>G	ENST00000326274.5	+	1	254	c.64T>G	c.(64-66)Tac>Gac	p.Y22D	VGLL2_ENST00000352536.3_Missense_Mutation_p.Y22D	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	22					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		CGCAGCCGCCTACACCCCCTA	0.587																																					p.Y22D		Atlas-SNP	.											.	VGLL2	18	.	0			c.T64G						PASS	.						104.0	83.0	90.0					6																	117586990		2203	4300	6503	SO:0001583	missense	245806	exon1			GCCGCCTACACCC	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"""vestigial like 2 (Drosophila)"""			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.64T>G	6.37:g.117586990T>G	ENSP00000320957:p.Tyr22Asp	53.0	0.0	0		68.0	24.0	0.352941	NM_182645	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	37	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336151	0.81801	.	.	ENSG00000170162	ENST00000352536;ENST00000326274	T	0.49720	0.77	5.17	5.17	0.71159	.	0.165964	0.41712	D	0.000824	T	0.49253	0.1546	L	0.34521	1.04	0.58432	D	0.999998	D;D	0.71674	0.997;0.998	D;D	0.78314	0.991;0.991	T	0.56637	-0.7946	10	0.72032	D	0.01	-6.5683	15.0077	0.71524	0.0:0.0:0.0:1.0	.	22;22	Q8N8G2-2;Q8N8G2	.;VGLL2_HUMAN	D	22	ENSP00000320957:Y22D	ENSP00000320957:Y22D	Y	+	1	0	VGLL2	117693683	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.294000	0.65687	1.961000	0.56991	0.460000	0.39030	TAC	.	.	none		0.587	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453	
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874240	31874240	+	Missense_Mutation	SNP	T	T	C	rs117415039	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31874240T>C	ENST00000334151.2	-	1	195	c.169A>G	c.(169-171)Agc>Ggc	p.S57G		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	57						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						GGACGGCAGCTGCGGTATCCA	0.527													T|||	28	0.00559105	0.0015	0.0072	5008	,	,		17008	0.0		0.0189	False		,,,				2504	0.002				p.S57G		Atlas-SNP	.											.	KRTAP19-5	32	.	0			c.A169G						PASS	.						111.0	109.0	110.0					21																	31874240		2203	4300	6503	SO:0001583	missense	337972	exon1			GGCAGCTGCGGTA	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"""Keratin associated proteins"""	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.169A>G	21.37:g.31874240T>C	ENSP00000334985:p.Ser57Gly	57.0	0.0	0		65.0	24.0	0.369231	NM_181611	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	37	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.296388	0.23650	.	.	ENSG00000186977	ENST00000334151	T	0.10288	2.89	5.16	3.98	0.46160	.	2.005650	0.03059	U	0.155572	T	0.11623	0.0283	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29579	-1.0007	9	0.87932	D	0	-2.7636	8.509	0.33206	0.8243:0.0:0.0:0.1757	.	57	Q3LI72	KR195_HUMAN	G	57	ENSP00000334985:S57G	ENSP00000334985:S57G	S	-	1	0	KRTAP19-5	30796111	0.634000	0.27190	0.008000	0.14137	0.219000	0.24729	1.424000	0.34848	0.904000	0.36572	-0.417000	0.06048	AGC	T|0.975;C|0.025	0.025	strong		0.527	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2		
ADARB2	105	hgsc.bcm.edu	37	10	1246060	1246060	+	Silent	SNP	C	C	T	rs138375235	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:1246060C>T	ENST00000381312.1	-	8	2035	c.1710G>A	c.(1708-1710)gcG>gcA	p.A570A	ADARB2_ENST00000381305.1_5'UTR|ADARB2_ENST00000381310.3_Silent_p.A79A	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	570	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		GGGACAGGAGCGCGCCCTGCA	0.692													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16229	0.0		0.002	False		,,,				2504	0.0				p.A570A		Atlas-SNP	.											.	ADARB2	95	.	0			c.G1710A						PASS	.	C		3,4293		0,3,2145	23.0	21.0	22.0		1710	-11.5	0.0	10	dbSNP_134	22	11,8469		0,11,4229	no	coding-synonymous	ADARB2	NM_018702.3		0,14,6374	TT,TC,CC		0.1297,0.0698,0.1096		570/740	1246060	14,12762	2148	4240	6388	SO:0001819	synonymous_variant	105	exon8			CAGGAGCGCGCCC	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1710G>A	10.37:g.1246060C>T		47.0	0.0	0		44.0	31.0	0.704545	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			C|0.997;T|0.003	0.003	strong		0.692	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79941511C>T	ENST00000306739.4	+	3	337	c.240C>T	c.(238-240)ccC>ccT	p.P80P	ASPSCR1_ENST00000581647.1_Silent_p.P80P|ASPSCR1_ENST00000306729.7_Silent_p.P80P|ASPSCR1_ENST00000580534.1_Silent_p.P3P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	80					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			AGATGGTGCCCGCTTCCCGGA	0.622			T	TFE3	alveolar soft part sarcoma								C|||	63	0.0125799	0.0015	0.0231	5008	,	,		12243	0.0		0.0209	False		,,,				2504	0.0245				p.P80P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	0			c.C240T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	80.0	63.0	69.0		240	-8.0	0.0	17	dbSNP_120	69	162,8438	76.3+/-139.0	2,158,4140	no	coding-synonymous	ASPSCR1	NM_024083.2		2,180,6321	TT,TC,CC		1.8837,0.4993,1.4147		80/554	79941511	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon3			GGTGCCCGCTTCC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.240C>T	17.37:g.79941511C>T		59.0	0.0	0		47.0	29.0	0.617021	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			C|0.988;T|0.012	0.012	strong		0.622	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
DYX1C1	161582	hgsc.bcm.edu	37	15	55789910	55789910	+	Splice_Site	SNP	C	C	T	rs17819126	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:55789910C>T	ENST00000321149.3	-	3	638	c.271G>A	c.(271-273)Gtt>Att	p.V91I	DYX1C1_ENST00000457155.2_Splice_Site_p.V91I|DYX1C1_ENST00000448430.2_Splice_Site_p.V91I|DYX1C1_ENST00000380679.1_Splice_Site_p.V91I|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Splice_Site_p.V91I	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	91	Mediates interaction with ESR1 and STUB1.		V -> I (in dbSNP:rs17819126). {ECO:0000269|PubMed:12954984}.		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		AAGAACTTACCACCCGTCACA	0.393													C|||	110	0.0219649	0.0053	0.0245	5008	,	,		15552	0.0		0.0596	False		,,,				2504	0.0266				p.V91I		Atlas-SNP	.											.	DYX1C1	54	.	0			c.G271A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	60,4326	56.2+/-92.4	0,60,2133	119.0	127.0	125.0		271,271,271	4.7	1.0	15	dbSNP_123	125	601,7983	158.6+/-212.1	23,555,3714	yes	missense-near-splice,missense-near-splice,missense-near-splice	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	29,29,29	23,615,5847	TT,TC,CC		7.0014,1.368,5.0964	benign,benign,benign	91/377,91/382,91/421	55789910	661,12309	2193	4292	6485	SO:0001630	splice_region_variant	161582	exon3			ACTTACCACCCGT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.271+1G>A	15.37:g.55789910C>T		49.0	0.0	0		47.0	29.0	0.617021	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	49	0.022435897435897436	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	41	0.05408970976253298	C	10.49	1.364727	0.24684	0.01368	0.070014	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	4.72	4.72	0.59763	HSP20-like chaperone (1);	0.252489	0.31279	U	0.007926	T	0.01287	0.0042	N	0.19112	0.55	0.34059	D	0.657104	B;B;B	0.15930	0.015;0.002;0.005	B;B;B	0.17433	0.009;0.002;0.018	T	0.11616	-1.0580	9	.	.	.	.	10.0731	0.42345	0.0:0.908:0.0:0.0919	rs17819126;rs52810117;rs17819126	91;91;91	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	I	91	ENSP00000403412:V91I;ENSP00000370054:V91I;ENSP00000402640:V91I;ENSP00000323275:V91I;ENSP00000299561:V91I	.	V	-	1	0	DYX1C1	53577202	0.965000	0.33210	0.999000	0.59377	0.426000	0.31534	1.565000	0.36386	2.450000	0.82876	0.561000	0.74099	GTT	C|0.959;T|0.041	0.041	strong		0.393	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	Missense_Mutation
TAS1R2	80834	hgsc.bcm.edu	37	1	19181279	19181279	+	Missense_Mutation	SNP	G	G	A	rs140330444		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19181279G>A	ENST00000375371.3	-	3	706	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	229					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ATGTCGCGCCGGGCCACGCGC	0.632													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.R229W		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C685T						PASS	.	G	TRP/ARG	0,4404		0,0,2202	41.0	38.0	39.0		685	-10.0	0.0	1	dbSNP_134	39	8,8590	5.7+/-21.5	0,8,4291	yes	missense	TAS1R2	NM_152232.2	101	0,8,6493	AA,AG,GG		0.093,0.0,0.0615	probably-damaging	229/840	19181279	8,12994	2202	4299	6501	SO:0001583	missense	80834	exon3			CGCGCCGGGCCAC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.685C>T	1.37:g.19181279G>A	ENSP00000364520:p.Arg229Trp	53.0	0.0	0		39.0	14.0	0.358974	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809991	0.31961	0.0	9.3E-4	ENSG00000179002	ENST00000375371	D	0.82984	-1.67	4.99	-9.98	0.00438	Extracellular ligand-binding receptor (1);	1.875720	0.02649	N	0.106245	T	0.77883	0.4197	L	0.39898	1.24	0.09310	N	1	D	0.61697	0.99	P	0.47376	0.545	T	0.76974	-0.2760	10	0.72032	D	0.01	.	11.3667	0.49677	0.0637:0.6431:0.1293:0.1639	.	229	Q8TE23	TS1R2_HUMAN	W	229	ENSP00000364520:R229W	ENSP00000364520:R229W	R	-	1	2	TAS1R2	19053866	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.329000	0.01111	-1.436000	0.01970	-0.270000	0.10280	CGG	G|1.000;A|0.000	0.000	weak		0.632	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
LAMA5	3911	hgsc.bcm.edu	37	20	60898891	60898891	+	Silent	SNP	C	C	T	rs138911913		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60898891C>T	ENST00000252999.3	-	44	5856	c.5790G>A	c.(5788-5790)ctG>ctA	p.L1930L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1930	Laminin EGF-like 18. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGCCGCCTCGCAGGACACAGC	0.687													.|||	1	0.000199681	0.0	0.0	5008	,	,		15565	0.0		0.001	False		,,,				2504	0.0				p.L1930L		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5790A						PASS	.	C		1,4363		0,1,2181	21.0	23.0	22.0		5790	-2.0	0.1	20	dbSNP_134	22	32,8540		0,32,4254	no	coding-synonymous	LAMA5	NM_005560.3		0,33,6435	TT,TC,CC		0.3733,0.0229,0.2551		1930/3696	60898891	33,12903	2182	4286	6468	SO:0001819	synonymous_variant	3911	exon44			GCCTCGCAGGACA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5790G>A	20.37:g.60898891C>T		78.0	0.0	0		51.0	23.0	0.45098	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.999;T|0.001	0.001	strong		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SSX3	10214	hgsc.bcm.edu	37	X	48213499	48213499	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48213499C>T	ENST00000298396.2	-	4	267	c.215G>A	c.(214-216)cGt>cAt	p.R72H	SSX3_ENST00000376895.1_5'Flank|SSX3_ENST00000376893.3_Missense_Mutation_p.R72H	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	72	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(1)|lung(9)	13						CCGTTTATTACGCATGAAAGA	0.478																																					p.R72H	Colon(37;227 826 19399 40970 48007)	Atlas-SNP	.											.	SSX3	64	.	0			c.G215A						PASS	.						135.0	120.0	125.0					X																	48213499		2203	4300	6503	SO:0001583	missense	10214	exon4			TTATTACGCATGA	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.215G>A	X.37:g.48213499C>T	ENSP00000298396:p.Arg72His	187.0	0.0	0		278.0	109.0	0.392086	NM_021014	O60223|Q5JQZ3|Q9BRW7	Missense_Mutation	SNP	ENST00000298396.2	37	CCDS14291.1	.	.	.	.	.	.	.	.	.	.	c	0.954	-0.705443	0.03255	.	.	ENSG00000165584	ENST00000298396;ENST00000376893	T;T	0.09630	3.01;2.96	1.52	-0.417	0.12347	Krueppel-associated box (2);Krueppel-associated box-related (1);	2.446520	0.01248	N	0.008799	T	0.08447	0.0210	N	0.25647	0.755	0.09310	N	1	B;B	0.14438	0.01;0.003	B;B	0.11329	0.006;0.002	T	0.30119	-0.9989	10	0.35671	T	0.21	.	4.0257	0.09687	0.0:0.5359:0.0:0.4641	.	72;72	Q9BRW7;Q99909	.;SSX3_HUMAN	H	72	ENSP00000298396:R72H;ENSP00000366090:R72H	ENSP00000298396:R72H	R	-	2	0	SSX3	48098443	0.000000	0.05858	0.005000	0.12908	0.020000	0.10135	-0.082000	0.11304	-0.233000	0.09797	-1.164000	0.01763	CGT	.	.	none		0.478	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102516487	102516487	+	Silent	SNP	G	G	A	rs35079638	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102516487G>A	ENST00000360184.4	+	77	13928	c.13764G>A	c.(13762-13764)acG>acA	p.T4588T	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4588					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						TTCCCCTGACGCAGCTGCGCT	0.567													.|||	5	0.000998403	0.0008	0.0014	5008	,	,		21568	0.0		0.003	False		,,,				2504	0.0				p.T4588T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G13764A						PASS	.	G		0,4406		0,0,2203	90.0	80.0	83.0		13764	-9.7	0.7	14	dbSNP_126	83	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	DYNC1H1	NM_001376.4		0,10,6493	AA,AG,GG		0.1163,0.0,0.0769		4588/4647	102516487	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon77			CCTGACGCAGCTG	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.13764G>A	14.37:g.102516487G>A		87.0	0.0	0		91.0	52.0	0.571429	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
PALD1	27143	hgsc.bcm.edu	37	10	72298745	72298745	+	Missense_Mutation	SNP	C	C	T	rs117244352	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72298745C>T	ENST00000263563.6	+	13	1818	c.1550C>T	c.(1549-1551)aCg>aTg	p.T517M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	517						cytosol (GO:0005829)											ATCTACGGCACGGCCCAGCCC	0.701													C|||	33	0.00658946	0.0015	0.0058	5008	,	,		16036	0.0		0.0249	False		,,,				2504	0.002				p.T517M		Atlas-SNP	.											.	.	.	.	0			c.C1550T						PASS	.	C	MET/THR	9,4397	15.5+/-35.6	0,9,2194	46.0	51.0	49.0		1550	-5.5	0.0	10	dbSNP_132	49	125,8473	63.5+/-125.6	1,123,4175	yes	missense	KIAA1274	NM_014431.2	81	1,132,6369	TT,TC,CC		1.4538,0.2043,1.0305	benign	517/857	72298745	134,12870	2203	4299	6502	SO:0001583	missense	27143	exon13			ACGGCACGGCCCA	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.1550C>T	10.37:g.72298745C>T	ENSP00000263563:p.Thr517Met	115.0	0.0	0		99.0	49.0	0.494949	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	21	0.009615384615384616	1	0.0020325203252032522	0	0.0	0	0.0	20	0.026385224274406333	c	0.509	-0.867379	0.02590	0.002043	0.014538	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.30182	1.54	5.01	-5.46	0.02608	.	0.342769	0.36066	N	0.002808	T	0.04770	0.0129	N	0.12422	0.21	0.23266	N	0.998011	B	0.20550	0.046	B	0.20184	0.028	T	0.06023	-1.0850	10	0.31617	T	0.26	-2.6083	14.93	0.70908	0.0:0.4702:0.0:0.5298	.	517	Q9ULE6	PALD_HUMAN	M	517	ENSP00000263563:T517M	ENSP00000263563:T517M	T	+	2	0	KIAA1274	71968751	0.084000	0.21492	0.013000	0.15412	0.480000	0.33159	0.407000	0.21049	-1.036000	0.03287	-1.137000	0.01932	ACG	C|0.990;T|0.010	0.010	strong		0.701	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
TMEM144	55314	hgsc.bcm.edu	37	4	159161513	159161513	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:159161513G>A	ENST00000296529.6	+	10	1265	c.745G>A	c.(745-747)Gcc>Acc	p.A249T	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	249						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CTACTTTCTGGCCTACTGCAT	0.358																																					p.A249T		Atlas-SNP	.											.	TMEM144	34	.	0			c.G745A						PASS	.						123.0	112.0	116.0					4																	159161513		2203	4300	6503	SO:0001583	missense	55314	exon10			TTTCTGGCCTACT	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.745G>A	4.37:g.159161513G>A	ENSP00000296529:p.Ala249Thr	117.0	0.0	0		89.0	46.0	0.516854	NM_018342	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	37	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771943	0.49680	.	.	ENSG00000164124	ENST00000296529	T	0.70164	-0.46	5.35	4.49	0.54785	.	0.484301	0.22175	N	0.063597	T	0.59074	0.2167	M	0.63843	1.955	0.46167	D	0.998902	B	0.33318	0.408	B	0.37601	0.254	T	0.51148	-0.8742	10	0.12430	T	0.62	-29.0069	5.6699	0.17717	0.1618:0.1716:0.6666:0.0	.	249	Q7Z5S9	TM144_HUMAN	T	249	ENSP00000296529:A249T	ENSP00000296529:A249T	A	+	1	0	TMEM144	159380963	1.000000	0.71417	0.981000	0.43875	0.967000	0.64934	3.462000	0.53042	1.216000	0.43427	0.467000	0.42956	GCC	.	.	none		0.358	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342	
DGCR2	9993	hgsc.bcm.edu	37	22	19028744	19028744	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19028744G>A	ENST00000263196.7	-	9	1470	c.1223C>T	c.(1222-1224)aCg>aTg	p.T408M	DGCR2_ENST00000537045.1_Missense_Mutation_p.T367M|DGCR2_ENST00000545799.1_3'UTR	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	408					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					CGTGAGGCCCGTGCCAAACCC	0.587																																					p.T408M		Atlas-SNP	.											.	DGCR2	45	.	0			c.C1223T						PASS	.						91.0	79.0	83.0					22																	19028744		2203	4300	6503	SO:0001583	missense	9993	exon9			AGGCCCGTGCCAA	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1223C>T	22.37:g.19028744G>A	ENSP00000263196:p.Thr408Met	72.0	0.0	0		72.0	4.0	0.0555556	NM_005137	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571021	0.86542	.	.	ENSG00000070413	ENST00000537045;ENST00000263196	T;D	0.97352	0.76;-4.35	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.98340	0.9449	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98951	1.0794	10	0.87932	D	0	.	20.0384	0.97572	0.0:0.0:1.0:0.0	.	364;408	B7Z3T5;P98153	.;IDD_HUMAN	M	367;408	ENSP00000440062:T367M;ENSP00000263196:T408M	ENSP00000263196:T408M	T	-	2	0	DGCR2	17408744	1.000000	0.71417	0.970000	0.41538	0.412000	0.31113	9.744000	0.98853	2.837000	0.97791	0.655000	0.94253	ACG	.	.	none		0.587	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137	
SF3B6	51639	hgsc.bcm.edu	37	2	24291323	24291323	+	Silent	SNP	G	G	A	rs41281479	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:24291323G>A	ENST00000233468.4	-	3	369	c.156C>T	c.(154-156)aaC>aaT	p.N52N		NM_016047.3	NP_057131.1														NS(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTCAGGTGTGTTCCCCCTGG	0.378													G|||	3	0.000599042	0.0	0.0	5008	,	,		16944	0.0		0.003	False		,,,				2504	0.0				p.N52N		Atlas-SNP	.											.	SF3B14	6	.	0			c.C156T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	135.0	124.0	128.0		156	3.2	1.0	2	dbSNP_127	128	64,8536	39.3+/-95.6	1,62,4237	no	coding-synonymous	SF3B14	NM_016047.3		1,71,6431	AA,AG,GG		0.7442,0.2043,0.5613		52/126	24291323	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			AGGTGTGTTCCCC																												ENST00000233468.4:c.156C>T	2.37:g.24291323G>A		110.0	0.0	0		100.0	49.0	0.49	NM_016047		Silent	SNP	ENST00000233468.4	37	CCDS1707.1																																																																																			G|0.997;A|0.003	0.003	strong		0.378	SF3B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246826.1		
RGAG1	57529	hgsc.bcm.edu	37	X	109696758	109696758	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:109696758T>G	ENST00000465301.2	+	3	3159	c.2913T>G	c.(2911-2913)gcT>gcG	p.A971A	RGAG1_ENST00000540313.1_Silent_p.A971A	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	971										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CAGCCATGGCTTCTGGAGAGA	0.512																																					p.A971A		Atlas-SNP	.											.	RGAG1	168	.	0			c.T2913G						PASS	.						144.0	138.0	140.0					X																	109696758		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			CATGGCTTCTGGA	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2913T>G	X.37:g.109696758T>G		62.0	0.0	0		71.0	24.0	0.338028	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			.	.	none		0.512	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769	
USP37	57695	hgsc.bcm.edu	37	2	219360656	219360656	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219360656T>C	ENST00000258399.3	-	14	1711	c.1299A>G	c.(1297-1299)ttA>ttG	p.L433L	USP37_ENST00000454775.1_Silent_p.L433L|USP37_ENST00000415516.1_Silent_p.L361L|USP37_ENST00000418019.1_Silent_p.L433L	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	433	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)		AACACTGACTTAAAAATTCAT	0.348																																					p.L433L		Atlas-SNP	.											.	USP37	76	.	0			c.A1299G						PASS	.						64.0	67.0	66.0					2																	219360656		2203	4300	6503	SO:0001819	synonymous_variant	57695	exon14			CTGACTTAAAAAT	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.1299A>G	2.37:g.219360656T>C		77.0	0.0	0		59.0	21.0	0.355932	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Silent	SNP	ENST00000258399.3	37	CCDS2418.1																																																																																			.	.	none		0.348	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935	
KNDC1	85442	hgsc.bcm.edu	37	10	135027195	135027195	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135027195C>T	ENST00000304613.3	+	25	4511	c.4490C>T	c.(4489-4491)gCc>gTc	p.A1497V	KNDC1_ENST00000368572.2_Missense_Mutation_p.A1499V			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1497	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		AACTCACGGGCCCTGGGCGTC	0.602																																					p.A1497V		Atlas-SNP	.											.	KNDC1	155	.	0			c.C4490T						PASS	.						94.0	77.0	83.0					10																	135027195		2203	4300	6503	SO:0001583	missense	85442	exon25			CACGGGCCCTGGG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4490C>T	10.37:g.135027195C>T	ENSP00000304437:p.Ala1497Val	61.0	0.0	0		52.0	10.0	0.192308	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.267975	0.59540	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.29142	1.58;1.58	4.26	4.26	0.50523	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.241819	0.34932	N	0.003571	T	0.46054	0.1373	L	0.47716	1.5	0.45330	D	0.998325	D	0.64830	0.994	D	0.67103	0.949	T	0.35276	-0.9795	10	0.41790	T	0.15	-25.7247	14.5448	0.68020	0.0:1.0:0.0:0.0	.	1497	Q76NI1	VKIND_HUMAN	V	1497;1499	ENSP00000304437:A1497V;ENSP00000357561:A1499V	ENSP00000304437:A1497V	A	+	2	0	KNDC1	134877185	1.000000	0.71417	0.998000	0.56505	0.282000	0.26991	2.812000	0.47994	2.093000	0.63338	0.313000	0.20887	GCC	.	.	none		0.602	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
RECQL5	9400	hgsc.bcm.edu	37	17	73657118	73657118	+	Silent	SNP	C	C	T	rs149970344		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73657118C>T	ENST00000317905.5	-	6	1062	c.903G>A	c.(901-903)gtG>gtA	p.V301V	RECQL5_ENST00000423245.2_Silent_p.V274V|RECQL5_ENST00000584999.1_Silent_p.V301V|RECQL5_ENST00000420326.2_Silent_p.V301V|RECQL5_ENST00000340830.5_Silent_p.V301V	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	301	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			AGTCGTTCTGCACCAGCGTTC	0.498								Other identified genes with known or suspected DNA repair function																													p.V301V		Atlas-SNP	.											.	RECQL5	77	.	0			c.G903A						PASS	.	C	,,	1,4405	2.1+/-5.4	0,1,2202	164.0	134.0	144.0		903,903,903	0.8	1.0	17	dbSNP_134	144	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RECQL5	NM_001003715.3,NM_001003716.3,NM_004259.6	,,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,,	301/436,301/411,301/992	73657118	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	9400	exon6			GTTCTGCACCAGC	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.903G>A	17.37:g.73657118C>T		152.0	0.0	0		155.0	61.0	0.393548	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			C|1.000;T|0.000	0.000	weak		0.498	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
PKN3	29941	hgsc.bcm.edu	37	9	131469190	131469190	+	Missense_Mutation	SNP	C	C	A	rs56251280	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131469190C>A	ENST00000291906.4	+	5	932	c.539C>A	c.(538-540)gCg>gAg	p.A180E	RN7SL560P_ENST00000577943.1_RNA	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	180			A -> E (in dbSNP:rs56251280). {ECO:0000269|PubMed:17344846}.		epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GAGCTGCTGGCGGAGGAGCTA	0.647													C|||	9	0.00179712	0.0	0.0043	5008	,	,		20063	0.0		0.004	False		,,,				2504	0.002				p.A180E		Atlas-SNP	.											.	PKN3	62	.	0			c.C539A						PASS	.	C	GLU/ALA	3,4401	8.1+/-20.4	0,3,2199	49.0	53.0	51.0		539	0.7	0.2	9	dbSNP_129	51	53,8547	33.3+/-86.6	0,53,4247	yes	missense	PKN3	NM_013355.3	107	0,56,6446	AA,AC,CC		0.6163,0.0681,0.4306	benign	180/890	131469190	56,12948	2202	4300	6502	SO:0001583	missense	29941	exon5			TGCTGGCGGAGGA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.539C>A	9.37:g.131469190C>A	ENSP00000291906:p.Ala180Glu	49.0	0.0	0		60.0	33.0	0.55	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	14.24	2.475101	0.43942	6.81E-4	0.006163	ENSG00000160447	ENST00000291906	T	0.30714	1.52	5.18	0.681	0.17986	.	.	.	.	.	T	0.28928	0.0718	L	0.36672	1.1	0.25043	N	0.991189	P;D	0.55172	0.917;0.97	P;P	0.60236	0.834;0.871	T	0.14671	-1.0464	9	0.66056	D	0.02	.	7.5493	0.27786	0.0:0.4389:0.0:0.5611	rs56251280	180;180	Q05BU1;Q6P5Z2	.;PKN3_HUMAN	E	180	ENSP00000291906:A180E	ENSP00000291906:A180E	A	+	2	0	PKN3	130509011	0.983000	0.35010	0.242000	0.24170	0.746000	0.42486	2.163000	0.42377	0.060000	0.16281	0.561000	0.74099	GCG	C|0.996;A|0.004	0.004	strong		0.647	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
BCL2A1	597	hgsc.bcm.edu	37	15	80263051	80263051	+	Silent	SNP	G	G	A	rs147879852		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80263051G>A	ENST00000267953.3	-	1	737	c.411C>T	c.(409-411)aaC>aaT	p.N137N	BCL2A1_ENST00000335661.6_Silent_p.N137N	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	137					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.N137N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CCCAGCCTCCGTTTTGCCTTA	0.368																																					p.N137N		Atlas-SNP	.											BCL2A1,colon,carcinoma,0,1	BCL2A1	28	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C411T						PASS	.	G	,	0,4406		0,0,2203	111.0	116.0	114.0		411,411	-8.2	0.1	15	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	BCL2A1	NM_001114735.1,NM_004049.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	137/164,137/176	80263051	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	597	exon1			GCCTCCGTTTTGC		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.411C>T	15.37:g.80263051G>A		160.0	0.0	0		187.0	94.0	0.502674	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Silent	SNP	ENST00000267953.3	37	CCDS10312.1																																																																																			G|1.000;A|0.000	0.000	weak		0.368	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
DNAH5	1767	hgsc.bcm.edu	37	5	13788927	13788927	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:13788927T>G	ENST00000265104.4	-	51	8649	c.8545A>C	c.(8545-8547)Agt>Cgt	p.S2849R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2849					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCTACCAAACTTACTAAAGCC	0.423									Kartagener syndrome																												p.S2849R		Atlas-SNP	.											.	DNAH5	868	.	0			c.A8545C						PASS	.						124.0	118.0	120.0					5																	13788927		2203	4300	6503	SO:0001583	missense	1767	exon51	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCAAACTTACTAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8545A>C	5.37:g.13788927T>G	ENSP00000265104:p.Ser2849Arg	207.0	0.0	0		199.0	37.0	0.18593	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	6.870	0.529813	0.13127	.	.	ENSG00000039139	ENST00000265104	T	0.23348	1.91	6.06	2.34	0.29019	.	0.290888	0.41823	N	0.000811	T	0.11965	0.0291	N	0.16266	0.395	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35674	-0.9779	10	0.09843	T	0.71	.	7.2973	0.26401	0.0:0.1272:0.1225:0.7503	.	2849	Q8TE73	DYH5_HUMAN	R	2849	ENSP00000265104:S2849R	ENSP00000265104:S2849R	S	-	1	0	DNAH5	13841927	0.173000	0.23056	0.000000	0.03702	0.990000	0.78478	1.723000	0.38053	0.169000	0.19679	0.533000	0.62120	AGT	.	.	none		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DHX32	55760	hgsc.bcm.edu	37	10	127548215	127548215	+	Missense_Mutation	SNP	G	G	A	rs201005566		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127548215G>A	ENST00000284690.3	-	3	1296	c.806C>T	c.(805-807)tCg>tTg	p.S269L	DHX32_ENST00000284688.6_Missense_Mutation_p.S269L	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	269						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTTCTCACCCGAGTGGTGAAT	0.383																																					p.S269L		Atlas-SNP	.											.	DHX32	67	.	0			c.C806T						PASS	.	G	LEU/SER	0,4406		0,0,2203	63.0	67.0	65.0		806	4.8	1.0	10		65	2,8598	3.0+/-9.4	0,2,4298	yes	missense	DHX32	NM_018180.2	145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	269/744	127548215	2,13004	2203	4300	6503	SO:0001583	missense	55760	exon3			TCACCCGAGTGGT		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"""DEAH-boxes"""	16717	protein-coding gene	gene with protein product		607960	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"""	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.806C>T	10.37:g.127548215G>A	ENSP00000284690:p.Ser269Leu	84.0	0.0	0		66.0	34.0	0.515152	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation	SNP	ENST00000284690.3	37	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253871	0.59212	0.0	2.33E-4	ENSG00000089876	ENST00000284690;ENST00000284688	T;T	0.08634	3.07;3.07	4.84	4.84	0.62591	.	0.122763	0.53938	D	0.000053	T	0.10035	0.0246	L	0.42744	1.35	0.24376	N	0.994816	P;P	0.52170	0.951;0.84	B;B	0.40134	0.32;0.17	T	0.10613	-1.0622	10	0.87932	D	0	-16.7608	17.1401	0.86750	0.0:0.0:1.0:0.0	.	269;269	Q7L7V1-2;Q7L7V1	.;DHX32_HUMAN	L	269	ENSP00000284690:S269L;ENSP00000284688:S269L	ENSP00000284688:S269L	S	-	2	0	DHX32	127538205	0.997000	0.39634	0.989000	0.46669	0.996000	0.88848	8.758000	0.91663	2.512000	0.84698	0.655000	0.94253	TCG	.	.	weak		0.383	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180	
CARKD	55739	hgsc.bcm.edu	37	13	111287893	111287893	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:111287893G>C	ENST00000309957.2	+	8	744	c.730G>C	c.(730-732)Gtc>Ctc	p.V244L	CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000458711.2_Missense_Mutation_p.V113L|CARKD_ENST00000424185.2_Missense_Mutation_p.V134L	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						CGTGACGGTGGTCCAGAAAGG	0.602																																					p.V244L		Atlas-SNP	.											.	CARKD	36	.	0			c.G730C						PASS	.						152.0	138.0	143.0					13																	111287893		2203	4300	6503	SO:0001583	missense	55739	exon8			ACGGTGGTCCAGA	AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.730G>C	13.37:g.111287893G>C	ENSP00000311984:p.Val244Leu	91.0	0.0	0		55.0	40.0	0.727273	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118803	0.37436	.	.	ENSG00000213995	ENST00000458711;ENST00000424185;ENST00000439607;ENST00000309957	T;T;T	0.23147	1.92;1.92;1.92	4.86	4.86	0.63082	Uncharacterised domain, carbohydrate kinase-related (3);	0.063290	0.64402	D	0.000006	T	0.21387	0.0515	N	0.20845	0.615	0.80722	D	1	D;P;B;B;B	0.55385	0.971;0.627;0.071;0.34;0.025	P;B;B;B;B	0.51079	0.658;0.329;0.047;0.085;0.047	T	0.02471	-1.1154	10	0.12430	T	0.62	-35.4382	11.1693	0.48563	0.086:0.0:0.914:0.0	.	113;134;226;244;244	B4DQR1;Q8IW45-4;B4DKX7;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	L	113;134;226;244	ENSP00000412789:V113L;ENSP00000413191:V134L;ENSP00000311984:V244L	ENSP00000311984:V244L	V	+	1	0	CARKD	110085894	1.000000	0.71417	0.063000	0.19743	0.245000	0.25701	3.457000	0.53007	2.210000	0.71456	0.462000	0.41574	GTC	.	.	none		0.602	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
C12orf40	283461	hgsc.bcm.edu	37	12	40041723	40041723	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40041723T>A	ENST00000324616.5	+	6	668	c.514T>A	c.(514-516)Tct>Act	p.S172T	C12orf40_ENST00000405531.3_Missense_Mutation_p.S172T|C12orf40_ENST00000398716.1_Missense_Mutation_p.S95T	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	172										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AAATTTCACATCTGGAATAGC	0.338																																					p.S172T		Atlas-SNP	.											C12orf40,NS,carcinoma,-1,1	C12orf40	118	1	0			c.T514A						scavenged	.						83.0	79.0	80.0					12																	40041723		1825	4077	5902	SO:0001583	missense	283461	exon6			TTCACATCTGGAA	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.514T>A	12.37:g.40041723T>A	ENSP00000317671:p.Ser172Thr	118.0	1.0	0.00847458		103.0	56.0	0.543689	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	2.128	-0.399903	0.04865	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.43688	0.94;0.95	3.74	1.92	0.25849	.	0.567024	0.14880	N	0.293000	T	0.20981	0.0505	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.17018	-1.0383	10	0.62326	D	0.03	.	6.0078	0.19557	0.0:0.7653:0.0:0.2347	.	172	Q86WS4	CL040_HUMAN	T	172;95;172	ENSP00000383897:S172T;ENSP00000317671:S172T	ENSP00000317671:S172T	S	+	1	0	C12orf40	38327990	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.012000	0.13287	0.565000	0.29255	-0.251000	0.11542	TCT	.	.	none		0.338	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
TRANK1	9881	hgsc.bcm.edu	37	3	36873866	36873866	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:36873866T>A	ENST00000429976.2	-	21	7323	c.7076A>T	c.(7075-7077)cAc>cTc	p.H2359L	TRANK1_ENST00000428977.2_Missense_Mutation_p.H1809L|TRANK1_ENST00000301807.6_Missense_Mutation_p.H1809L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2359							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GAAGCACAGGTGGGTCTTGTC	0.473																																					p.H2359L		Atlas-SNP	.											.	TRANK1	398	.	0			c.A7076T						PASS	.						97.0	102.0	100.0					3																	36873866		1954	4144	6098	SO:0001583	missense	9881	exon21			CACAGGTGGGTCT	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.7076A>T	3.37:g.36873866T>A	ENSP00000416168:p.His2359Leu	273.0	0.0	0		270.0	153.0	0.566667	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	10.14	1.267837	0.23136	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34472	1.36;1.77;1.36	5.16	3.97	0.46021	.	0.108511	0.40469	N	0.001086	T	0.27967	0.0689	L	0.32530	0.975	0.32062	N	0.595608	B	0.31680	0.335	B	0.30401	0.115	T	0.30621	-0.9972	10	0.44086	T	0.13	.	12.5047	0.55975	0.0:0.0:0.1394:0.8606	.	2359	O15050	TRNK1_HUMAN	L	1809;2359;1809	ENSP00000416826:H1809L;ENSP00000416168:H2359L;ENSP00000301807:H1809L	ENSP00000301807:H1809L	H	-	2	0	TRANK1	36848870	1.000000	0.71417	0.995000	0.50966	0.400000	0.30750	4.152000	0.58111	0.878000	0.35920	0.459000	0.35465	CAC	.	.	none		0.473	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
RFX8	731220	hgsc.bcm.edu	37	2	102019129	102019129	+	Silent	SNP	C	C	T	rs201832728		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:102019129C>T	ENST00000376826.2	-	14	1352	c.1353G>A	c.(1351-1353)gaG>gaA	p.E451E	RFX8_ENST00000428343.1_Silent_p.E338E			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|stomach(1)	3						TCCCCATGtcctcctcctcct	0.478													c|||	1	0.000199681	0.0	0.0	5008	,	,		19522	0.0		0.001	False		,,,				2504	0.0				p.E338E		Atlas-SNP	.											.	RFX8	16	.	0			c.G1014A						PASS	.	C		1,1383		0,1,691	63.0	58.0	59.0		1014	-0.4	0.1	2		59	5,3177		0,5,1586	yes	coding-synonymous	RFX8	NM_001145664.1		0,6,2277	TT,TC,CC		0.1571,0.0723,0.1314		338/474	102019129	6,4560	692	1591	2283	SO:0001819	synonymous_variant	731220	exon11			CATGTCCTCCTCC	AK124976	CCDS46376.1	2q11.2	2012-11-15	2012-11-15		ENSG00000196460	ENSG00000196460			37253	protein-coding gene	gene with protein product			"""regulatory factor X, 8"", ""RFX gene family member 8, lacking RFX DNA binding domain"""				Standard	NM_001145664		Approved	FLJ42986	uc010yvx.1	Q6ZV50	OTTHUMG00000130693	ENST00000376826.2:c.1353G>A	2.37:g.102019129C>T		81.0	0.0	0		89.0	42.0	0.47191	NM_001145664	B4DQ32	Silent	SNP	ENST00000376826.2	37																																																																																				.	.	weak		0.478	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
LRP2	4036	hgsc.bcm.edu	37	2	170063380	170063380	+	Missense_Mutation	SNP	T	T	C	rs35413340	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170063380T>C	ENST00000263816.3	-	39	7135	c.6850A>G	c.(6850-6852)Act>Gct	p.T2284A		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2284					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TCAAAAACAGTGATGCCATAA	0.398													T|||	3	0.000599042	0.0	0.0014	5008	,	,		21566	0.0		0.002	False		,,,				2504	0.0				p.T2284A		Atlas-SNP	.											.	LRP2	751	.	0			c.A6850G						PASS	.	T	ALA/THR	2,4404	4.2+/-10.8	0,2,2201	126.0	129.0	128.0		6850	5.9	1.0	2	dbSNP_126	128	21,8579	16.0+/-53.3	0,21,4279	yes	missense	LRP2	NM_004525.2	58	0,23,6480	CC,CT,TT		0.2442,0.0454,0.1768	possibly-damaging	2284/4656	170063380	23,12983	2203	4300	6503	SO:0001583	missense	4036	exon39			AAACAGTGATGCC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.6850A>G	2.37:g.170063380T>C	ENSP00000263816:p.Thr2284Ala	85.0	0.0	0		79.0	36.0	0.455696	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	4.072	0.011210	0.07912	4.54E-4	0.002442	ENSG00000081479	ENST00000263816	D	0.89681	-2.55	5.89	5.89	0.94794	Six-bladed beta-propeller, TolB-like (1);	0.045886	0.85682	D	0.000000	T	0.77432	0.4129	N	0.20328	0.56	0.80722	D	1	P	0.35192	0.489	B	0.26310	0.068	T	0.77696	-0.2491	10	0.02654	T	1	.	16.3127	0.82898	0.0:0.0:0.0:1.0	rs35413340	2284	P98164	LRP2_HUMAN	A	2284	ENSP00000263816:T2284A	ENSP00000263816:T2284A	T	-	1	0	LRP2	169771626	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.885000	0.48570	2.246000	0.74042	0.533000	0.62120	ACT	T|0.999;C|0.001	0.001	strong		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PAQR7	164091	hgsc.bcm.edu	37	1	26189517	26189517	+	Missense_Mutation	SNP	C	C	T	rs6689014	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26189517C>T	ENST00000374296.3	-	2	1480	c.814G>A	c.(814-816)Ggg>Agg	p.G272R	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	272			G -> R (in dbSNP:rs6689014).		multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			breast(3)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		TGGCCCTGCCCGAAGACATGG	0.587													C|||	19	0.00379393	0.0	0.0029	5008	,	,		20920	0.0		0.0169	False		,,,				2504	0.0				p.G272R	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-SNP	.											.	PAQR7	23	.	0			c.G814A						PASS	.	C	ARG/GLY	7,4399	12.9+/-30.5	0,7,2196	51.0	51.0	51.0		814	4.3	1.0	1	dbSNP_116	51	76,8524	43.6+/-101.6	0,76,4224	yes	missense	PAQR7	NM_178422.5	125	0,83,6420	TT,TC,CC		0.8837,0.1589,0.6382	probably-damaging	272/347	26189517	83,12923	2203	4300	6503	SO:0001583	missense	164091	exon2			CCTGCCCGAAGAC		CCDS267.1	1p35.3	2012-08-10			ENSG00000182749	ENSG00000182749			23146	protein-coding gene	gene with protein product	"""membrane progestin receptor alpha"""	607779					Standard	NM_178422		Approved	mSR, MPRA	uc001bkx.3	Q86WK9	OTTHUMG00000007373	ENST00000374296.3:c.814G>A	1.37:g.26189517C>T	ENSP00000363414:p.Gly272Arg	101.0	0.0	0		113.0	57.0	0.504425	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	37	CCDS267.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	21.1	4.099077	0.76983	0.001589	0.008837	ENSG00000182749	ENST00000374296	T	0.37752	1.18	5.2	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.57021	0.2025	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70572	-0.4835	10	0.72032	D	0.01	-19.195	14.8991	0.70664	0.1446:0.8554:0.0:0.0	rs6689014;rs52808965;rs6689014	272	Q86WK9	MPRA_HUMAN	R	272	ENSP00000363414:G272R	ENSP00000363414:G272R	G	-	1	0	PAQR7	26062104	1.000000	0.71417	0.993000	0.49108	0.775000	0.43874	5.912000	0.69948	1.390000	0.46547	-0.182000	0.12963	GGG	C|0.995;T|0.005	0.005	strong		0.587	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422	
HIST4H4	121504	hgsc.bcm.edu	37	12	14923887	14923887	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:14923887G>A	ENST00000539745.1	-	1	178	c.132C>T	c.(130-132)gtC>gtT	p.V44V	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	44					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						AAATGCGCTTGACGCCCCCAC	0.612											OREG0021698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V44V		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C132T						PASS	.						61.0	57.0	59.0					12																	14923887		2203	4300	6503	SO:0001819	synonymous_variant	121504	exon1			GCGCTTGACGCCC	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"""Histones / Replication-dependent"""	20510	protein-coding gene	gene with protein product		615069	"""histone 4, H4"""			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.132C>T	12.37:g.14923887G>A		71.0	0.0	0	698	83.0	5.0	0.060241	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000539745.1	37	CCDS8665.1																																																																																			.	.	none		0.612	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054	
TMEM69	51249	hgsc.bcm.edu	37	1	46159157	46159157	+	Silent	SNP	C	C	T	rs61735666	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46159157C>T	ENST00000372025.4	+	3	1481	c.324C>T	c.(322-324)ttC>ttT	p.F108F	TMEM69_ENST00000496366.1_3'UTR|RP11-767N6.7_ENST00000430643.1_RNA	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	108						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					TAATCCCCTTCGTTGCTCCAC	0.458													C|||	26	0.00519169	0.0015	0.0	5008	,	,		21035	0.0		0.005	False		,,,				2504	0.0194				p.F108F		Atlas-SNP	.											.	TMEM69	20	.	0			c.C324T						PASS	.	C		5,3905		0,5,1950	167.0	164.0	165.0		324	-7.3	0.0	1	dbSNP_129	165	54,8254		1,52,4101	no	coding-synonymous	TMEM69	NM_016486.3		1,57,6051	TT,TC,CC		0.65,0.1279,0.4829		108/248	46159157	59,12159	1955	4154	6109	SO:0001819	synonymous_variant	51249	exon3			CCCCTTCGTTGCT	BC040289, BC013608	CCDS41325.1	1p34.1	2008-02-05	2005-08-17	2005-08-17	ENSG00000159596	ENSG00000159596			28035	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 154"""	C1orf154			Standard	NM_016486		Approved	FLJ21029	uc001cor.1	Q5SWH9	OTTHUMG00000040993	ENST00000372025.4:c.324C>T	1.37:g.46159157C>T		84.0	0.0	0		92.0	38.0	0.413043	NM_016486	Q3SWW5|Q7Z2G0|Q9P0P9	Silent	SNP	ENST00000372025.4	37	CCDS41325.1																																																																																			C|0.996;T|0.004	0.004	strong		0.458	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486	
ZNF318	24149	hgsc.bcm.edu	37	6	43305991	43305991	+	Silent	SNP	A	A	T	rs374528550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:43305991A>T	ENST00000361428.2	-	10	5822	c.5745T>A	c.(5743-5745)gtT>gtA	p.V1915V	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1915					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CCTCACTAACAACTGAAACTC	0.438																																					p.V1915V		Atlas-SNP	.											.	ZNF318	175	.	0			c.T5745A						PASS	.	A		0,4406		0,0,2203	98.0	98.0	98.0		5745	4.0	0.1	6		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF318	NM_014345.2		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		1915/2280	43305991	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	24149	exon10			ACTAACAACTGAA	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.5745T>A	6.37:g.43305991A>T		96.0	0.0	0		102.0	58.0	0.568627	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																			.	.	weak		0.438	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
SYNCRIP	10492	hgsc.bcm.edu	37	6	86332210	86332210	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:86332210A>C	ENST00000369622.3	-	8	1498	c.998T>G	c.(997-999)gTt>gGt	p.V333G	SYNCRIP_ENST00000355238.6_Missense_Mutation_p.V333G	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	333					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		CTTTGCCATAACCTCAGGATC	0.448																																					p.V333G		Atlas-SNP	.											.	SYNCRIP	80	.	0			c.T998G						PASS	.						221.0	215.0	217.0					6																	86332210		2203	4300	6503	SO:0001583	missense	10492	exon8			GCCATAACCTCAG	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"""RNA binding motif (RRM) containing"""	16918	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein Q"""					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.998T>G	6.37:g.86332210A>C	ENSP00000358635:p.Val333Gly	93.0	0.0	0		113.0	6.0	0.0530973	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	37	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.636864	0.67130	.	.	ENSG00000135316	ENST00000355238;ENST00000369622	T;T	0.74526	-0.85;-0.85	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	L	0.41079	1.255	0.80722	D	1	B;B;B;B;B	0.28667	0.219;0.122;0.089;0.193;0.219	B;B;B;B;B	0.31442	0.054;0.078;0.13;0.066;0.054	T	0.65800	-0.6080	10	0.87932	D	0	.	16.0711	0.80936	1.0:0.0:0.0:0.0	.	333;235;181;333;333	O60506;B7Z645;O60506-5;O60506-3;B2R8Z8	HNRPQ_HUMAN;.;.;.;.	G	333	ENSP00000347380:V333G;ENSP00000358635:V333G	ENSP00000347380:V333G	V	-	2	0	SYNCRIP	86388929	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.287000	0.95975	2.197000	0.70478	0.482000	0.46254	GTT	.	.	none		0.448	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372	
GBP1	2633	hgsc.bcm.edu	37	1	89523844	89523844	+	Silent	SNP	G	G	A	rs141095851	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89523844G>A	ENST00000370473.4	-	6	924	c.705C>T	c.(703-705)tgC>tgT	p.C235C	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	235	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CAAAGACAAAGCATTTTTTCT	0.413													.|||	3	0.000599042	0.0	0.0	5008	,	,		16439	0.0		0.003	False		,,,				2504	0.0				p.C235C		Atlas-SNP	.											.	GBP1	68	.	0			c.C705T						PASS	.	G		5,4401	8.1+/-20.4	0,5,2198	150.0	165.0	160.0		705	2.6	1.0	1	dbSNP_134	160	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	GBP1	NM_002053.2		0,19,6484	AA,AG,GG		0.1628,0.1135,0.1461		235/593	89523844	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	2633	exon6			GACAAAGCATTTT	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.705C>T	1.37:g.89523844G>A		106.0	0.0	0		125.0	62.0	0.496	NM_002053	D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	CCDS718.1																																																																																			G|0.999;A|0.001	0.001	strong		0.413	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124610	26124610	+	Silent	SNP	G	G	A	rs139293879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26124610G>A	ENST00000602637.1	+	1	180	c.150G>A	c.(148-150)gtG>gtA	p.V50V	HIST1H2AC_ENST00000377791.2_Silent_p.V50V|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	50						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						GCGCGCCGGTGTACCTGGCGG	0.672																																					p.V50V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G150A						PASS	.						44.0	46.0	45.0					6																	26124610		2203	4299	6502	SO:0001819	synonymous_variant	8334	exon1			GCCGGTGTACCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.150G>A	6.37:g.26124610G>A		100.0	0.0	0		92.0	24.0	0.26087	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			G|1.000;C|0.000	.	alt		0.672	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
PNPLA1	285848	hgsc.bcm.edu	37	6	36269675	36269675	+	Silent	SNP	T	T	A	rs201231660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:36269675T>A	ENST00000394571.2	+	6	813	c.813T>A	c.(811-813)atT>atA	p.I271I	PNPLA1_ENST00000388715.3_Silent_p.I176I|PNPLA1_ENST00000312917.5_Silent_p.I185I	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	271					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						AGAGAGTGATTTTCCCCCGGG	0.512											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		20927	0.0		0.001	False		,,,				2504	0.0				p.I271I		Atlas-SNP	.											.	PNPLA1	92	.	0			c.T813A						PASS	.	T	,,	1,4405	2.1+/-5.4	0,1,2202	79.0	82.0	81.0		555,813,528	-5.1	0.9	6		81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	,,	0,1,6502	AA,AT,TT		0.0,0.0227,0.0077	,,	185/447,271/533,176/438	36269675	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	285848	exon6			AGTGATTTTCCCC		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.813T>A	6.37:g.36269675T>A		108.0	0.0	0	861	87.0	61.0	0.701149	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																			T|1.000;A|0.000	0.000	strong		0.512	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
TLR3	7098	hgsc.bcm.edu	37	4	187004078	187004078	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187004078A>C	ENST00000296795.3	+	4	1342	c.1238A>C	c.(1237-1239)aAc>aCc	p.N413T	TLR3_ENST00000504367.1_Missense_Mutation_p.N136T	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	413					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		CACATACTCAACCTAACCAAG	0.378																																					p.N413T		Atlas-SNP	.											.	TLR3	83	.	0			c.A1238C						PASS	.						61.0	57.0	58.0					4																	187004078		2203	4300	6503	SO:0001583	missense	7098	exon4			TACTCAACCTAAC	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1238A>C	4.37:g.187004078A>C	ENSP00000296795:p.Asn413Thr	101.0	0.0	0		86.0	26.0	0.302326	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.452831	0.43531	.	.	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020;ENST00000504367	T;T;T	0.39997	1.75;1.05;1.75	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.53061	0.1773	M	0.72118	2.19	0.80722	D	1	P	0.41569	0.755	P	0.46144	0.505	T	0.57917	-0.7728	10	0.72032	D	0.01	.	16.1132	0.81278	1.0:0.0:0.0:0.0	.	413	O15455	TLR3_HUMAN	T	413;349;413;136	ENSP00000296795:N413T;ENSP00000423386:N349T;ENSP00000423684:N136T	ENSP00000296795:N413T	N	+	2	0	TLR3	187241072	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	9.339000	0.96797	2.208000	0.71279	0.455000	0.32223	AAC	.	.	none		0.378	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
POLR1A	25885	hgsc.bcm.edu	37	2	86317012	86317012	+	Missense_Mutation	SNP	C	C	G	rs146078741	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86317012C>G	ENST00000263857.6	-	4	851	c.473G>C	c.(472-474)cGg>cCg	p.R158P	POLR1A_ENST00000409681.1_Missense_Mutation_p.R158P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	158					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TAATTCCTCCCGAATTTCAGA	0.453													C|||	24	0.00479233	0.0	0.0173	5008	,	,		20367	0.0		0.0119	False		,,,				2504	0.0				p.R158P		Atlas-SNP	.											.	POLR1A	137	.	0			c.G473C						PASS	.	C	PRO/ARG	7,3743		0,7,1868	164.0	152.0	156.0		473	4.0	1.0	2	dbSNP_134	156	74,8140		1,72,4034	yes	missense	POLR1A	NM_015425.3	103	1,79,5902	GG,GC,CC		0.9009,0.1867,0.677	benign	158/1721	86317012	81,11883	1875	4107	5982	SO:0001583	missense	25885	exon4			TCCTCCCGAATTT	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.473G>C	2.37:g.86317012C>G	ENSP00000263857:p.Arg158Pro	152.0	0.0	0		69.0	18.0	0.26087	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	14	0.00641025641025641	0	0.0	6	0.016574585635359115	0	0.0	8	0.010554089709762533	C	4.071	0.011112	0.07912	0.001867	0.009009	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.22539	1.95;1.95	5.2	4.04	0.47022	RNA polymerase Rpb1, domain 1 (1);	0.483471	0.23437	N	0.048199	T	0.08980	0.0222	N	0.24115	0.695	0.28088	N	0.93191	P;B	0.43287	0.802;0.293	P;B	0.48488	0.579;0.204	T	0.03875	-1.0996	10	0.30854	T	0.27	-17.9919	7.1854	0.25797	0.0:0.1768:0.0:0.8232	.	158;158	B9ZVN9;O95602	.;RPA1_HUMAN	P	158	ENSP00000263857:R158P;ENSP00000386300:R158P	ENSP00000263857:R158P	R	-	2	0	POLR1A	86170523	1.000000	0.71417	1.000000	0.80357	0.076000	0.17211	1.894000	0.39768	0.911000	0.36747	-0.294000	0.09567	CGG	C|0.991;G|0.009	0.009	strong		0.453	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637049	111637049	+	Missense_Mutation	SNP	C	C	T	rs554564263		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111637049C>T	ENST00000527614.1	-	1	102	c.37G>A	c.(37-39)Gca>Aca	p.A13T	PPP2R1B_ENST00000341980.6_Missense_Mutation_p.A13T|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.A13T|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.A13T|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.A13T	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	13					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CCACCCGCTGCTCCTGGGCCG	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		7436	0.001		0.0	False		,,,				2504	0.0				p.A13T		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.G37A						PASS	.						64.0	63.0	63.0					11																	111637049		2201	4297	6498	SO:0001583	missense	5519	exon1			CCGCTGCTCCTGG	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.37G>A	11.37:g.111637049C>T	ENSP00000437193:p.Ala13Thr	24.0	0.0	0		35.0	17.0	0.485714	NM_001177562	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159377	0.78226	.	.	ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000341980;ENST00000393055	.	.	.	5.23	4.29	0.51040	.	0.363905	0.30076	N	0.010474	T	0.53400	0.1794	L	0.28192	0.835	0.80722	D	1	B;B;B;P;B	0.49447	0.131;0.357;0.084;0.924;0.137	B;B;B;P;B	0.57776	0.016;0.246;0.034;0.827;0.075	T	0.52756	-0.8533	9	0.46703	T	0.11	-0.7229	10.9852	0.47518	0.1867:0.8133:0.0:0.0	.	13;13;13;13;13	A8MY67;F8W8G1;B4DWW5;P30154;P30154-2	.;.;.;2AAB_HUMAN;.	T	13	.	ENSP00000311344:A13T	A	-	1	0	PPP2R1B	111142259	0.983000	0.35010	0.071000	0.20095	0.022000	0.10575	1.945000	0.40273	1.138000	0.42230	0.557000	0.71058	GCA	.	.	none		0.672	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
PVRL1	5818	hgsc.bcm.edu	37	11	119548402	119548402	+	Missense_Mutation	SNP	C	C	T	rs78809001	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119548402C>T	ENST00000264025.3	-	3	1126	c.596G>A	c.(595-597)cGg>cAg	p.R199Q	PVRL1_ENST00000340882.2_Missense_Mutation_p.R199Q|PVRL1_ENST00000341398.2_Missense_Mutation_p.R199Q|PVRL1_ENST00000524510.1_5'UTR	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	199	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		ATTGGGGTTCCGGATCTCCTG	0.597													c|||	17	0.00339457	0.0008	0.0101	5008	,	,		19081	0.0		0.0089	False		,,,				2504	0.0				p.R199Q		Atlas-SNP	.											.	PVRL1	133	.	0			c.G596A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	8,4390	12.9+/-30.5	0,8,2191	156.0	139.0	145.0		596,596,596	5.2	1.0	11	dbSNP_131	145	117,8473	62.1+/-124.0	0,117,4178	yes	missense,missense,missense	PVRL1	NM_002855.4,NM_203285.1,NM_203286.1	43,43,43	0,125,6369	TT,TC,CC		1.362,0.1819,0.9624	probably-damaging,probably-damaging,probably-damaging	199/518,199/459,199/353	119548402	125,12863	2199	4295	6494	SO:0001583	missense	5818	exon3			GGGTTCCGGATCT	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.596G>A	11.37:g.119548402C>T	ENSP00000264025:p.Arg199Gln	192.0	0.0	0		208.0	34.0	0.163462	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	c	17.34	3.364188	0.61513	0.001819	0.01362	ENSG00000110400	ENST00000341398;ENST00000264025;ENST00000340882	T;T;T	0.76186	-1.0;-1.0;-1.0	5.21	5.21	0.72293	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.055119	0.64402	D	0.000001	T	0.72700	0.3493	L	0.53249	1.67	0.43628	D	0.996013	D;D;D	0.89917	0.996;0.997;1.0	B;P;P	0.57911	0.423;0.559;0.829	T	0.75502	-0.3295	9	.	.	.	.	11.2519	0.49031	0.0:0.9162:0.0:0.0838	.	199;199;199	Q15223-3;Q15223;Q15223-2	.;PVRL1_HUMAN;.	Q	199	ENSP00000344974:R199Q;ENSP00000264025:R199Q;ENSP00000345289:R199Q	.	R	-	2	0	PVRL1	119053612	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	2.997000	0.49457	2.450000	0.82876	0.556000	0.70494	CGG	C|0.991;T|0.009	0.009	strong		0.597	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
ABCC4	10257	hgsc.bcm.edu	37	13	95715014	95715014	+	Silent	SNP	A	A	G	rs11568655	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95715014A>G	ENST00000376887.4	-	26	3424	c.3310T>C	c.(3310-3312)Ttg>Ctg	p.L1104L	ABCC4_ENST00000412704.1_Silent_p.L1057L	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1104	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	TCAGTTGTCAAGATCTTATCA	0.423													A|||	130	0.0259585	0.093	0.0086	5008	,	,		16253	0.0		0.001	False		,,,				2504	0.0				p.L1104L		Atlas-SNP	.											.	ABCC4	248	.	0			c.T3310C						PASS	.	A		368,4038	187.8+/-214.3	17,334,1852	130.0	122.0	124.0		3310	6.2	1.0	13	dbSNP_126	124	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ABCC4	NM_005845.3		17,336,6150	GG,GA,AA		0.0233,8.3522,2.8448		1104/1326	95715014	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon26			TTGTCAAGATCTT	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3310T>C	13.37:g.95715014A>G		71.0	0.0	0		81.0	43.0	0.530864	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			A|0.966;G|0.034	0.034	strong		0.423	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
ADIPOQ	9370	hgsc.bcm.edu	37	3	186572089	186572089	+	Missense_Mutation	SNP	T	T	C	rs17366743	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186572089T>C	ENST00000412955.2	+	3	472	c.331T>C	c.(331-333)Tac>Cac	p.Y111H	ADIPOQ_ENST00000320741.2_Missense_Mutation_p.Y111H|ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.Y111H			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	111	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		Y -> H (in dbSNP:rs17366743). {ECO:0000269|PubMed:12354786}.		adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		TGCCTATGTATACCGCTCAGC	0.517													T|||	57	0.0113818	0.0015	0.0072	5008	,	,		19832	0.0		0.0378	False		,,,				2504	0.0123				p.Y111H		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.T331C	GRCh37	CM056934	ADIPOQ	M	rs17366743	PASS	.	T	HIS/TYR,HIS/TYR	34,4372	39.2+/-71.8	0,34,2169	162.0	145.0	151.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	331,331	3.1	0.9	3	dbSNP_123	151	275,8325	104.0+/-165.0	7,261,4032	yes	missense,missense	ADIPOQ	NM_001177800.1,NM_004797.3	83,83	7,295,6201	CC,CT,TT		3.1977,0.7717,2.3758	benign,benign	111/245,111/245	186572089	309,12697	2203	4300	6503	SO:0001583	missense	9370	exon4			TATGTATACCGCT	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"""Endogenous ligands"""	13633	protein-coding gene	gene with protein product	"""adipose most abundant gene transcript 1"", ""adiponectin precursor"""	605441	"""adipocyte, C1Q and collagen domain containing"""	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.331T>C	3.37:g.186572089T>C	ENSP00000405611:p.Tyr111His	159.0	0.0	0		173.0	69.0	0.398844	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	37	CCDS3284.1	38	0.0173992673992674	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	32	0.04221635883905013	T	12.88	2.071182	0.36566	0.007717	0.031977	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.83506	-1.73;-1.73;-1.73	5.45	3.07	0.35406	Tumour necrosis factor-like (1);Complement C1q protein (2);	0.316112	0.30630	N	0.009220	T	0.38321	0.1036	L	0.33245	0.995	0.22620	N	0.99893	B	0.12630	0.006	B	0.15052	0.012	T	0.32771	-0.9894	10	0.15066	T	0.55	.	7.1499	0.25604	0.0:0.2542:0.0:0.7458	rs17366743;rs52807560;rs17366743	111	Q15848	ADIPO_HUMAN	H	111	ENSP00000405611:Y111H;ENSP00000320709:Y111H;ENSP00000389814:Y111H	ENSP00000320709:Y111H	Y	+	1	0	ADIPOQ	188054783	0.750000	0.28316	0.905000	0.35620	0.821000	0.46438	1.011000	0.29911	0.467000	0.27218	0.459000	0.35465	TAC	T|0.981;C|0.019	0.019	strong		0.517	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797	
RAET1L	154064	hgsc.bcm.edu	37	6	150342155	150342155	+	Missense_Mutation	SNP	C	C	T	rs148198102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:150342155C>T	ENST00000367341.1	-	3	516	c.517G>A	c.(517-519)Gag>Aag	p.E173K	RAET1L_ENST00000286380.2_Missense_Mutation_p.E173K			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	173	MHC class I alpha-2 like. {ECO:0000250}.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TTGTCATTCTCCCACTTTTCT	0.483													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		21805	0.0		0.008	False		,,,				2504	0.0051				p.E173K		Atlas-SNP	.											.	RAET1L	21	.	0			c.G517A						PASS	.	C	LYS/GLU	10,4396	16.8+/-37.8	0,10,2193	296.0	259.0	272.0		517	-0.0	0.0	6	dbSNP_134	272	84,8516	47.6+/-106.9	0,84,4216	no	missense	RAET1L	NM_130900.2	56	0,94,6409	TT,TC,CC		0.9767,0.227,0.7227	possibly-damaging	173/247	150342155	94,12912	2203	4300	6503	SO:0001583	missense	154064	exon3			CATTCTCCCACTT	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.517G>A	6.37:g.150342155C>T	ENSP00000356310:p.Glu173Lys	307.0	1.0	0.00325733		297.0	144.0	0.484848	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	37	CCDS5224.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	c	12.88	2.069672	0.36470	0.00227	0.009767	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.09445	2.98;2.98	1.91	-0.0121	0.13989	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.10594	0.0259	M	0.72576	2.205	0.09310	N	1	D	0.58620	0.983	P	0.59424	0.857	T	0.08743	-1.0707	9	0.87932	D	0	.	4.1768	0.10356	0.0:0.6012:0.0:0.3988	.	173	Q5VY80	RET1L_HUMAN	K	173	ENSP00000356310:E173K;ENSP00000286380:E173K	ENSP00000286380:E173K	E	-	1	0	RAET1L	150383848	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.064000	0.11636	-0.026000	0.13895	0.491000	0.48974	GAG	C|0.994;T|0.006	0.006	strong		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
PPP2R3B	28227	hgsc.bcm.edu	37	X	322294	322294	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:322294G>A	ENST00000390665.3	-	2	374	c.356C>T	c.(355-357)cCg>cTg	p.P119L		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	119					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GCTCGTGGCCGGGGGCAGAGG	0.582																																					p.P119L		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.C356T						PASS	.	G	LEU/PRO	6,4186		0,6,2090	145.0	177.0	166.0		356	1.6	0.0	X		166	0,8416		0,0,4208	no	missense	PPP2R3B	NM_013239.4	98	0,6,6298	AA,AG,GG		0.0,0.1431,0.0476	possibly-damaging	119/576	322294	6,12602	2096	4208	6304	SO:0001583	missense	28227	exon2			GTGGCCGGGGGCA	AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"""Pseudoautosomal regions / PAR1"", ""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	13417	protein-coding gene	gene with protein product		300339	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"""	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.356C>T	X.37:g.322294G>A	ENSP00000375080:p.Pro119Leu	310.0	0.0	0		241.0	161.0	0.66805	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Missense_Mutation	SNP	ENST00000390665.3	37	CCDS14104.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671721	0.29693	0.001431	0.0	ENSG00000167393	ENST00000390665;ENST00000381625	T;T	0.32515	1.45;1.45	1.62	1.62	0.23740	.	0.285142	0.27172	U	0.020583	T	0.23846	0.0577	L	0.61218	1.895	0.20196	N	0.999928	P	0.47762	0.9	B	0.33521	0.165	T	0.23511	-1.0186	10	0.87932	D	0	.	8.9681	0.35890	0.0:0.0:1.0:0.0	.	119	Q9Y5P8	P2R3B_HUMAN	L	119;91	ENSP00000375080:P119L;ENSP00000371038:P91L	ENSP00000371038:P91L	P	-	2	0	PPP2R3B	242294	1.000000	0.71417	0.013000	0.15412	0.073000	0.16967	4.432000	0.59922	0.579000	0.29504	0.115000	0.15696	CCG	.	.	weak		0.582	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239	
PTK2	5747	hgsc.bcm.edu	37	8	141711117	141711117	+	Missense_Mutation	SNP	G	G	C	rs185796736		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:141711117G>C	ENST00000522684.1	-	26	2601	c.2372C>G	c.(2371-2373)tCt>tGt	p.S791C	PTK2_ENST00000519465.1_Missense_Mutation_p.S419C|PTK2_ENST00000517887.1_Missense_Mutation_p.S835C|PTK2_ENST00000340930.3_Missense_Mutation_p.S791C|PTK2_ENST00000430260.2_Missense_Mutation_p.S101C|PTK2_ENST00000535192.1_Missense_Mutation_p.S745C|PTK2_ENST00000519419.1_Missense_Mutation_p.S835C|PTK2_ENST00000395218.2_Missense_Mutation_p.S791C|PTK2_ENST00000538769.1_Missense_Mutation_p.S459C|PTK2_ENST00000521059.1_Missense_Mutation_p.S791C	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	791	Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CAATACTGTAGAGTCCTGGAA	0.433													G|||	1	0.000199681	0.0	0.0	5008	,	,		18321	0.0		0.001	False		,,,				2504	0.0				p.S813C		Atlas-SNP	.											.	PTK2	311	.	0			c.C2438G						PASS	.						68.0	61.0	63.0					8																	141711117		2203	4300	6503	SO:0001583	missense	5747	exon26			ACTGTAGAGTCCT	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2372C>G	8.37:g.141711117G>C	ENSP00000429911:p.Ser791Cys	131.0	0.0	0		140.0	67.0	0.478571	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.73	3.881225	0.72294	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986;ENST00000522424;ENST00000521562	T;T;T;T;T;T;T;T;T;T;T;T	0.76968	-1.02;-1.06;-1.02;-1.02;-1.02;-1.03;-1.0;-1.02;-1.0;-1.02;1.42;-1.02	5.91	5.91	0.95273	.	0.450679	0.27856	N	0.017569	T	0.76018	0.3929	L	0.36672	1.1	0.40191	D	0.977405	P;P;P;D;P;P;P;P;P;P	0.57257	0.938;0.517;0.899;0.979;0.94;0.953;0.517;0.488;0.938;0.833	P;B;P;B;B;B;P;P;P;P	0.46718	0.502;0.325;0.502;0.394;0.428;0.319;0.447;0.525;0.502;0.502	T	0.75563	-0.3274	10	0.38643	T	0.18	.	19.9156	0.97061	0.0:0.0:1.0:0.0	.	791;486;711;791;813;745;743;639;459;419	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	C	791;745;419;835;791;743;791;712;486;463;791;459;835;101;489;101;101	ENSP00000429911:S791C;ENSP00000438009:S745C;ENSP00000429170:S419C;ENSP00000429082:S835C;ENSP00000429474:S791C;ENSP00000378644:S791C;ENSP00000428492:S463C;ENSP00000341189:S791C;ENSP00000445742:S459C;ENSP00000429129:S835C;ENSP00000403416:S101C;ENSP00000430603:S489C	ENSP00000341189:S791C	S	-	2	0	PTK2	141780299	1.000000	0.71417	0.873000	0.34254	0.911000	0.54048	4.259000	0.58828	2.808000	0.96608	0.655000	0.94253	TCT	G|0.999;C|0.001	0.001	strong		0.433	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
SSPO	23145	hgsc.bcm.edu	37	7	149492640	149492640	+	RNA	SNP	G	G	A	rs372238122		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:149492640G>A	ENST00000378016.2	+	0	6420							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCCTAGTGCCGGAGACTGGCT	0.617																																					p.P2140P		Atlas-SNP	.											.	.	.	.	0			c.G6420A						PASS	.	G		0,4254		0,0,2127	57.0	65.0	63.0		6424	2.8	0.0	7		63	1,8491		0,1,4245	no	coding-notMod3	SSPO	NM_198455.2		0,1,6372	AA,AG,GG		0.0118,0.0,0.0078			149492640	1,12745	2127	4246	6373			23145	exon43			AGTGCCGGAGACT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149492640G>A		115.0	0.0	0		109.0	58.0	0.53211	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ITGA11	22801	hgsc.bcm.edu	37	15	68654003	68654003	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:68654003A>G	ENST00000315757.7	-	5	483	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Missense_Mutation_p.Y133H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	133					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GTGGTGTAGTAGGAGCTCCCA	0.567																																					p.Y133H		Atlas-SNP	.											.	ITGA11	110	.	0			c.T397C						PASS	.						59.0	58.0	58.0					15																	68654003		1961	4143	6104	SO:0001583	missense	22801	exon5			TGTAGTAGGAGCT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.397T>C	15.37:g.68654003A>G	ENSP00000327290:p.Tyr133His	37.0	0.0	0		57.0	5.0	0.0877193	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.812724	0.32053	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.71934	-0.61;-0.61	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.76499	0.3996	L	0.47190	1.495	0.41168	D	0.986143	D;D	0.76494	0.997;0.999	D;D	0.72982	0.94;0.979	T	0.72250	-0.4348	10	0.15066	T	0.55	.	13.6022	0.62026	1.0:0.0:0.0:0.0	.	133;133	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	133	ENSP00000327290:Y133H;ENSP00000403392:Y133H	ENSP00000327290:Y133H	Y	-	1	0	ITGA11	66441057	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.080000	0.57620	1.856000	0.53863	0.459000	0.35465	TAC	.	.	none		0.567	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274867G>C	ENST00000290551.4	+	1	204	c.133G>C	c.(133-135)Gca>Cca	p.A45P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45P		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133C						PASS	.						11.0	13.0	13.0					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>C	1.37:g.203274867G>C	ENSP00000290551:p.Ala45Pro	90.0	0.0	0		81.0	30.0	0.37037	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163593	0.78226	.	.	ENSG00000159388	ENST00000290551	T	0.25085	1.82	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.52008	0.1708	M	0.82630	2.6	0.47374	D	0.999406	D	0.62365	0.991	D	0.64687	0.928	T	0.58222	-0.7674	10	0.51188	T	0.08	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	P	45	ENSP00000290551:A45P	ENSP00000290551:A45P	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171766135	171766135	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:171766135T>G	ENST00000311601.5	-	13	2144	c.1974A>C	c.(1972-1974)gaA>gaC	p.E658D	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	658					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	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)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGACTTGGTCTTCGCCCTGAG	0.587																																					p.E658D		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.A1974C						PASS	.						105.0	100.0	102.0					5																	171766135		2203	4300	6503	SO:0001583	missense	285590	exon13			TTGGTCTTCGCCC	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1974A>C	5.37:g.171766135T>G	ENSP00000309714:p.Glu658Asp	100.0	0.0	0		113.0	28.0	0.247788	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	T	6.943	0.543719	0.13250	.	.	ENSG00000174705	ENST00000311601	T	0.61627	0.09	4.94	1.31	0.21738	.	0.309439	0.34223	N	0.004160	T	0.29423	0.0733	N	0.12746	0.255	0.32639	N	0.520891	B	0.15141	0.012	B	0.14023	0.01	T	0.09862	-1.0655	9	.	.	.	-9.4913	2.9632	0.05899	0.1917:0.3214:0.0:0.487	.	658	A1X283	SPD2B_HUMAN	D	658	ENSP00000309714:E658D	.	E	-	3	2	SH3PXD2B	171698740	0.991000	0.36638	0.995000	0.50966	0.525000	0.34531	0.257000	0.18369	0.396000	0.25283	0.454000	0.30748	GAA	.	.	none		0.587	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963	
MUC2	4583	hgsc.bcm.edu	37	11	1097794	1097794	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1097794A>T	ENST00000441003.2	+	36	6914	c.6887A>T	c.(6886-6888)aAg>aTg	p.K2296M	MUC2_ENST00000361558.6_3'UTR	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4658					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GACCCCTCCAAGCCACACTGC	0.657																																					p.K2292M		Atlas-SNP	.											.	MUC2	614	.	0			c.A6875T						PASS	.						30.0	41.0	37.0					11																	1097794		2097	4203	6300	SO:0001583	missense	4583	exon37			CCTCCAAGCCACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6887A>T	11.37:g.1097794A>T	ENSP00000415183:p.Lys2296Met	74.0	0.0	0		68.0	5.0	0.0735294	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	9.090	1.001589	0.19121	.	.	ENSG00000198788	ENST00000441003	T	0.14766	2.48	3.88	2.71	0.32032	.	.	.	.	.	T	0.27933	0.0688	M	0.77313	2.365	0.20563	N	0.999886	D	0.61080	0.989	P	0.53809	0.735	T	0.07616	-1.0763	9	0.59425	D	0.04	.	9.7512	0.40477	0.8264:0.1736:0.0:0.0	.	2296	E7EUV1	.	M	2296	ENSP00000415183:K2296M	ENSP00000415183:K2296M	K	+	2	0	MUC2	1087794	1.000000	0.71417	0.887000	0.34795	0.669000	0.39330	5.420000	0.66441	0.510000	0.28216	0.459000	0.35465	AAG	.	.	none		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CLN8	2055	hgsc.bcm.edu	37	8	1719450	1719450	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:1719450G>C	ENST00000331222.4	+	2	477	c.230G>C	c.(229-231)aGc>aCc	p.S77T		NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	77	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				adult walking behavior (GO:0007628)|age-dependent response to oxidative stress (GO:0001306)|associative learning (GO:0008306)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|ceramide biosynthetic process (GO:0046513)|ceramide metabolic process (GO:0006672)|cholesterol metabolic process (GO:0008203)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|lipid biosynthetic process (GO:0008610)|lipid transport (GO:0006869)|lysosome organization (GO:0007040)|mitochondrial membrane organization (GO:0007006)|musculoskeletal movement (GO:0050881)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteolysis (GO:0045861)|negative regulation of transferase activity (GO:0051348)|nervous system development (GO:0007399)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|phospholipid metabolic process (GO:0006644)|photoreceptor cell maintenance (GO:0045494)|protein catabolic process (GO:0030163)|regulation of cell size (GO:0008361)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic motor neuron differentiation (GO:0021523)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		GGTGTTCAGAGCACAGCCGCA	0.612																																					p.S77T	Pancreas(155;338 1942 6138 10888 50612)	Atlas-SNP	.											.	CLN8	64	.	0			c.G230C						PASS	.						73.0	68.0	70.0					8																	1719450		2203	4300	6503	SO:0001583	missense	2055	exon2			TTCAGAGCACAGC	AF123761	CCDS5956.1	8p23.3	2014-09-17			ENSG00000182372	ENSG00000182372			2079	protein-coding gene	gene with protein product		607837	"""chromosome 8 open reading frame 61"""	EPMR, C8orf61		10508524	Standard	NM_018941		Approved	FLJ39417	uc003wpo.4	Q9UBY8	OTTHUMG00000090343	ENST00000331222.4:c.230G>C	8.37:g.1719450G>C	ENSP00000328182:p.Ser77Thr	140.0	0.0	0		160.0	18.0	0.1125	NM_018941	Q86U71|Q96I95	Missense_Mutation	SNP	ENST00000331222.4	37	CCDS5956.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.936506	0.52972	.	.	ENSG00000182372	ENST00000331222	D	0.87491	-2.26	5.06	5.06	0.68205	TRAM/LAG1/CLN8 homology domain (3);	0.131081	0.49305	U	0.000147	D	0.88183	0.6368	L	0.54323	1.7	0.54753	D	0.999987	P	0.51537	0.946	P	0.53146	0.719	D	0.84829	0.0801	10	0.07482	T	0.82	-1.7549	18.4221	0.90594	0.0:0.0:1.0:0.0	.	77	Q9UBY8	CLN8_HUMAN	T	77	ENSP00000328182:S77T	ENSP00000328182:S77T	S	+	2	0	CLN8	1706857	1.000000	0.71417	0.992000	0.48379	0.140000	0.21249	8.757000	0.91657	2.329000	0.79093	0.455000	0.32223	AGC	.	.	none		0.612	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941	
ZNF577	84765	hgsc.bcm.edu	37	19	52375854	52375854	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52375854T>G	ENST00000301399.5	-	7	1754	c.1389A>C	c.(1387-1389)acA>acC	p.T463T	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Silent_p.T404T|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.T404T	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	463					regulation of transcription, DNA-templated (GO:0006355)|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)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCACTTCATTTGTGAGGCTTA	0.363																																					p.T463T		Atlas-SNP	.											.	ZNF577	63	.	0			c.A1389C						PASS	.						59.0	57.0	57.0					19																	52375854		2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			TTCATTTGTGAGG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1389A>C	19.37:g.52375854T>G		63.0	0.0	0		73.0	18.0	0.246575	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.	.	none		0.363	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
LRP6	4040	hgsc.bcm.edu	37	12	12279735	12279735	+	Missense_Mutation	SNP	C	C	T	rs34815107	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12279735C>T	ENST00000261349.4	-	20	4278	c.4202G>A	c.(4201-4203)cGt>cAt	p.R1401H	LRP6_ENST00000543091.1_Missense_Mutation_p.R1356H|LRP6_ENST00000540415.1_Intron|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1401			R -> H (in dbSNP:rs34815107).		anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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 Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TCCCTTCATACGTGGACACAA	0.448													C|||	15	0.00299521	0.0113	0.0	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.R1401H		Atlas-SNP	.											.	LRP6	170	.	0			c.G4202A						PASS	.	C	HIS/ARG	72,4334	64.7+/-102.0	0,72,2131	194.0	161.0	172.0		4202	5.6	1.0	12	dbSNP_126	172	0,8600		0,0,4300	yes	missense	LRP6	NM_002336.2	29	0,72,6431	TT,TC,CC		0.0,1.6341,0.5536	benign	1401/1614	12279735	72,12934	2203	4300	6503	SO:0001583	missense	4040	exon20			TTCATACGTGGAC	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4202G>A	12.37:g.12279735C>T	ENSP00000261349:p.Arg1401His	110.0	0.0	0		93.0	46.0	0.494624	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	16.69	3.194168	0.58017	0.016341	0.0	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.44482	0.92;0.92	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000007	T	0.22322	0.0538	L	0.38175	1.15	0.53005	D	0.999968	B;B	0.13145	0.005;0.007	B;B	0.12156	0.002;0.007	T	0.04103	-1.0977	10	0.28530	T	0.3	.	19.6816	0.95965	0.0:1.0:0.0:0.0	rs34815107	1356;1401	F5H7J9;O75581	.;LRP6_HUMAN	H	1401;1356	ENSP00000261349:R1401H;ENSP00000442472:R1356H	ENSP00000261349:R1401H	R	-	2	0	LRP6	12171002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.510000	0.60455	2.646000	0.89796	0.563000	0.77884	CGT	C|0.994;T|0.006	0.006	strong		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
NPHP4	261734	hgsc.bcm.edu	37	1	6012866	6012866	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6012866T>G	ENST00000378156.4	-	7	969	c.704A>C	c.(703-705)aAg>aCg	p.K235T	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	235					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CGTGATGGGCTTCTGGAGGCG	0.577																																					p.K235T		Atlas-SNP	.											.	NPHP4	119	.	0			c.A704C						PASS	.						25.0	28.0	27.0					1																	6012866		1883	4106	5989	SO:0001583	missense	261734	exon7			ATGGGCTTCTGGA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.704A>C	1.37:g.6012866T>G	ENSP00000367398:p.Lys235Thr	42.0	0.0	0		42.0	11.0	0.261905	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	t	17.28	3.350455	0.61183	.	.	ENSG00000131697	ENST00000378156	D	0.88975	-2.45	5.04	5.04	0.67666	.	0.137440	0.47455	D	0.000235	D	0.92776	0.7703	M	0.75264	2.295	0.37280	D	0.907778	D	0.76494	0.999	D	0.71656	0.974	D	0.93997	0.7272	10	0.62326	D	0.03	.	8.8131	0.34978	0.0:0.0886:0.0:0.9114	.	235	O75161	NPHP4_HUMAN	T	235	ENSP00000367398:K235T	ENSP00000367398:K235T	K	-	2	0	NPHP4	5935453	0.995000	0.38212	0.977000	0.42913	0.809000	0.45718	2.595000	0.46197	1.892000	0.54788	0.459000	0.35465	AAG	.	.	none		0.577	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
IAH1	285148	hgsc.bcm.edu	37	2	9616161	9616161	+	Missense_Mutation	SNP	C	C	G	rs61732203	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:9616161C>G	ENST00000497473.1	+	2	164	c.127C>G	c.(127-129)Ctg>Gtg	p.L43V	IAH1_ENST00000545602.1_Intron|IAH1_ENST00000482918.1_5'UTR|IAH1_ENST00000489468.1_3'UTR|IAH1_ENST00000470914.1_Intron	NM_001039613.1	NP_001034702.1	Q2TAA2	IAH1_HUMAN	isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae)	43					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|large_intestine(2)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGCTGACAGGCTGGTCAGGTG	0.468													C|||	43	0.00858626	0.0015	0.0043	5008	,	,		19592	0.0		0.0348	False		,,,				2504	0.0031				p.L43V		Atlas-SNP	.											.	IAH1	12	.	0			c.C127G						PASS	.	C	VAL/LEU	11,3921		0,11,1955	104.0	105.0	104.0		127	5.8	1.0	2	dbSNP_129	104	218,8110		6,206,3952	yes	missense	IAH1	NM_001039613.1	32	6,217,5907	GG,GC,CC		2.6177,0.2798,1.8679	probably-damaging	43/249	9616161	229,12031	1966	4164	6130	SO:0001583	missense	285148	exon2			GACAGGCTGGTCA	BC111025	CCDS42651.1	2p25.1	2010-08-05			ENSG00000134330	ENSG00000134330			27696	protein-coding gene	gene with protein product						12477932	Standard	XR_426950		Approved		uc002qzr.3	Q2TAA2	OTTHUMG00000159076	ENST00000497473.1:c.127C>G	2.37:g.9616161C>G	ENSP00000417580:p.Leu43Val	170.0	0.0	0		179.0	178.0	0.994413	NM_001039613	B4DMV3	Missense_Mutation	SNP	ENST00000497473.1	37	CCDS42651.1	31	0.014194139194139194	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	27	0.03562005277044855	C	21.8	4.203472	0.79127	0.002798	0.026177	ENSG00000134330	ENST00000497473;ENST00000481688	T;T	0.25085	1.82;1.82	5.78	5.78	0.91487	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.000000	0.64402	U	0.000002	T	0.16214	0.0390	L	0.58428	1.81	0.80722	D	1	D	0.67145	0.996	D	0.66847	0.947	T	0.01786	-1.1274	10	0.72032	D	0.01	-0.4573	14.5371	0.67969	0.0:0.9301:0.0:0.0699	rs61732203	43	Q2TAA2	IAH1_HUMAN	V	43;18	ENSP00000417580:L43V;ENSP00000420532:L18V	ENSP00000420532:L18V	L	+	1	2	IAH1	9533612	0.993000	0.37304	0.981000	0.43875	0.980000	0.70556	3.057000	0.49931	2.894000	0.99253	0.591000	0.81541	CTG	C|0.982;G|0.018	0.018	strong		0.468	IAH1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353192.1	NM_001039613	
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29449819C>T	ENST00000389048.3	-	18	3942	c.3036G>A	c.(3034-3036)acG>acA	p.T1012T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1012			T -> M (in dbSNP:rs35073634). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T1012T(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CAGCCAGCACCGTCCCGTGGT	0.542			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	851	0.169928	0.2277	0.147	5008	,	,		21422	0.119		0.1928	False		,,,				2504	0.137				p.T1012T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - coding silent(1)	stomach(1)	c.G3036A						PASS	.	C		974,3432	366.4+/-317.8	105,764,1334	202.0	180.0	187.0		3036	-10.8	0.1	2	dbSNP_100	187	1492,7108	283.2+/-296.0	137,1218,2945	no	coding-synonymous	ALK	NM_004304.4		242,1982,4279	TT,TC,CC		17.3488,22.1062,18.9605		1012/1621	29449819	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	238	exon18	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGCACCGTCCCG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3036G>A	2.37:g.29449819C>T		126.0	0.0	0		119.0	60.0	0.504202	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			C|0.816;T|0.184	0.184	strong		0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
DYNC1I1	1780	hgsc.bcm.edu	37	7	95442624	95442624	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95442624T>A	ENST00000324972.6	+	4	533	c.340T>A	c.(340-342)Tca>Aca	p.S114T	DYNC1I1_ENST00000413338.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.S114T|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.S97T|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.S97T	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	114	Interaction with DCTN1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			AAGCCAAGACTCAGGCGATCT	0.418																																					p.S114T		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.T340A						PASS	.						76.0	74.0	74.0					7																	95442624		2203	4300	6503	SO:0001583	missense	1780	exon4			CAAGACTCAGGCG	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.340T>A	7.37:g.95442624T>A	ENSP00000320130:p.Ser114Thr	62.0	0.0	0		63.0	7.0	0.111111	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954071	0.53293	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000413338;ENST00000518089;ENST00000457059	T;T;T;T;T;T	0.76186	-0.67;-0.77;-1.0;-0.73;-0.79;-0.67	4.55	4.55	0.56014	.	0.146929	0.47093	D	0.000259	T	0.62829	0.2460	L	0.28649	0.875	0.58432	D	0.999992	B;B;P;B;P	0.36789	0.25;0.097;0.57;0.25;0.57	B;B;B;B;B	0.35413	0.041;0.09;0.142;0.041;0.202	T	0.63497	-0.6624	10	0.31617	T	0.26	-6.2365	14.9476	0.71044	0.0:0.0:0.0:1.0	.	97;114;97;114;97	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	T	97;114;97;114;97;97;97;97	ENSP00000392337:S97T;ENSP00000320130:S114T;ENSP00000438377:S97T;ENSP00000398118:S114T;ENSP00000352348:S97T;ENSP00000412444:S97T	ENSP00000320130:S114T	S	+	1	0	DYNC1I1	95280560	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.769000	0.85360	2.267000	0.75376	0.533000	0.62120	TCA	.	.	none		0.418	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
TMEM54	113452	hgsc.bcm.edu	37	1	33361552	33361552	+	Missense_Mutation	SNP	C	C	T	rs139394643	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33361552C>T	ENST00000373463.3	-	3	348	c.229G>A	c.(229-231)Gca>Aca	p.A77T	TMEM54_ENST00000475208.1_Intron|TMEM54_ENST00000329151.5_Intron	NM_033504.2	NP_277039.1	Q969K7	TMM54_HUMAN	transmembrane protein 54	77						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ACGATGGCTGCGATGCCTGAA	0.627													C|||	2	0.000399361	0.0008	0.0	5008	,	,		21423	0.0		0.001	False		,,,				2504	0.0				p.A77T		Atlas-SNP	.											.	TMEM54	12	.	0			c.G229A						PASS	.	C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	70.0	62.0	65.0		229	0.3	0.7	1	dbSNP_134	65	32,8568	21.6+/-65.8	0,32,4268	yes	missense	TMEM54	NM_033504.2	58	0,34,6469	TT,TC,CC		0.3721,0.0454,0.2614	benign	77/223	33361552	34,12972	2203	4300	6503	SO:0001583	missense	113452	exon3			TGGCTGCGATGCC		CCDS371.1	1p35-p34	2008-02-05			ENSG00000121900	ENSG00000121900			24143	protein-coding gene	gene with protein product						9500206	Standard	NM_033504		Approved	CAC-1	uc001bwi.1	Q969K7	OTTHUMG00000004016	ENST00000373463.3:c.229G>A	1.37:g.33361552C>T	ENSP00000362562:p.Ala77Thr	32.0	0.0	0		37.0	15.0	0.405405	NM_033504	Q6UV18|Q8IVD0|Q9UM12	Missense_Mutation	SNP	ENST00000373463.3	37	CCDS371.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.06	1.824482	0.32237	4.54E-4	0.003721	ENSG00000121900	ENST00000373463	T	0.41400	1.0	4.51	0.262	0.15597	.	0.776453	0.12444	N	0.468393	T	0.11024	0.0269	N	0.00538	-1.39	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.10154	-1.0642	10	0.25751	T	0.34	.	4.3725	0.11255	0.3239:0.4944:0.0:0.1818	.	77	Q969K7	TMM54_HUMAN	T	77	ENSP00000362562:A77T	ENSP00000362562:A77T	A	-	1	0	TMEM54	33134139	0.000000	0.05858	0.743000	0.31040	0.866000	0.49608	0.316000	0.19469	0.170000	0.19704	0.462000	0.41574	GCA	C|0.998;T|0.002	0.002	strong		0.627	TMEM54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011474.1	NM_033504	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101834386	101834386	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101834386G>A	ENST00000506729.1	-	1	334	c.163C>T	c.(163-165)Cca>Tca	p.P55S	SLCO6A1_ENST00000379807.3_Missense_Mutation_p.P55S|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.P55S|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.P55S|SLCO6A1_ENST00000514551.1_5'Flank|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.P55S			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		AAGGCCTCTGGAAGTAGTCTC	0.572																																					p.P55S		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C163T						PASS	.						154.0	170.0	165.0					5																	101834386		2203	4300	6503	SO:0001583	missense	133482	exon1			CCTCTGGAAGTAG	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.163C>T	5.37:g.101834386G>A	ENSP00000421339:p.Pro55Ser	103.0	0.0	0		122.0	5.0	0.0409836	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315767	0.40996	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.62498	0.57;0.57;0.24;0.02;0.02	3.52	-0.367	0.12541	.	16.882000	0.00166	N	0.000000	T	0.47600	0.1454	L	0.29908	0.895	0.09310	N	1	P;P;P	0.46142	0.873;0.799;0.799	B;B;B	0.40066	0.318;0.256;0.169	T	0.37478	-0.9704	10	0.39692	T	0.17	.	2.8587	0.05579	0.3443:0.0:0.4559:0.1998	.	55;55;55	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	S	55	ENSP00000421339:P55S;ENSP00000369135:P55S;ENSP00000373671:P55S;ENSP00000421990:P55S;ENSP00000369138:P55S	ENSP00000369135:P55S	P	-	1	0	SLCO6A1	101862285	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.165000	0.09968	-0.098000	0.12285	0.484000	0.47621	CCA	.	.	none		0.572	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
MUC17	140453	hgsc.bcm.edu	37	7	100686777	100686777	+	Missense_Mutation	SNP	C	C	T	rs138142210	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100686777C>T	ENST00000306151.4	+	3	12144	c.12080C>T	c.(12079-12081)aCg>aTg	p.T4027M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4027					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.T4027M(2)|p.T4027K(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCTGCATCAACGCTTTCTGCA	0.537													c|||	103	0.0205671	0.0	0.0173	5008	,	,		23075	0.0		0.0328	False		,,,				2504	0.0593				p.T4027M		Atlas-SNP	.											MUC17,NS,carcinoma,0,3	MUC17	804	3	3	Substitution - Missense(3)	prostate(1)|large_intestine(1)|lung(1)	c.C12080T						PASS	.		MET/THR	10,4396	17.9+/-39.9	0,10,2193	330.0	285.0	300.0		12080	-1.7	0.0	7	dbSNP_134	300	215,8385	90.4+/-152.6	2,211,4087	yes	missense	MUC17	NM_001040105.1	81	2,221,6280	TT,TC,CC		2.5,0.227,1.73	probably-damaging	4027/4494	100686777	225,12781	2203	4300	6503	SO:0001583	missense	140453	exon3			CATCAACGCTTTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.12080C>T	7.37:g.100686777C>T	ENSP00000302716:p.Thr4027Met	220.0	0.0	0		234.0	125.0	0.534188	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	c	1.187	-0.636447	0.03557	0.00227	0.025	ENSG00000169876	ENST00000306151	T	0.02158	4.42	1.69	-1.66	0.08265	.	.	.	.	.	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	1	P	0.46578	0.88	B	0.26864	0.074	T	0.51748	-0.8666	9	0.34782	T	0.22	.	5.0714	0.14609	0.0:0.3773:0.0:0.6227	.	4027	Q685J3	MUC17_HUMAN	M	4027	ENSP00000302716:T4027M	ENSP00000302716:T4027M	T	+	2	0	MUC17	100473497	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.697000	0.05098	-0.342000	0.08363	-0.359000	0.07587	ACG	C|0.983;T|0.017	0.017	strong		0.537	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
USP36	57602	hgsc.bcm.edu	37	17	76823425	76823425	+	Silent	SNP	G	G	T	rs143701541	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:76823425G>T	ENST00000542802.3	-	6	1034	c.591C>A	c.(589-591)atC>atA	p.I197I	USP36_ENST00000312010.6_Silent_p.I197I|USP36_ENST00000589424.1_Silent_p.I197I|USP36_ENST00000590546.2_Silent_p.I197I			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	197	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			AGTGTCGGGCGATCTCTAAAA	0.552													G|||	58	0.0115815	0.0015	0.0101	5008	,	,		12480	0.0		0.0308	False		,,,				2504	0.0184				p.I197I		Atlas-SNP	.											.	USP36	243	.	0			c.C591A						PASS	.	G		26,4380	31.7+/-61.6	0,26,2177	43.0	37.0	39.0		591	-7.7	0.8	17	dbSNP_134	39	261,8339	101.9+/-163.1	4,253,4043	no	coding-synonymous	USP36	NM_025090.3		4,279,6220	TT,TG,GG		3.0349,0.5901,2.2067		197/1124	76823425	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	57602	exon6			TCGGGCGATCTCT	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.591C>A	17.37:g.76823425G>T		27.0	0.0	0		38.0	22.0	0.578947	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																			G|0.980;T|0.020	0.020	strong		0.552	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
BPHL	670	hgsc.bcm.edu	37	6	3129402	3129402	+	Missense_Mutation	SNP	G	G	A	rs199698749	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:3129402G>A	ENST00000380379.5	+	4	551	c.502G>A	c.(502-504)Gtc>Atc	p.V168I	BPHL_ENST00000380375.3_Missense_Mutation_p.V151I|BPHL_ENST00000434640.1_Missense_Mutation_p.V151I|BPHL_ENST00000380368.2_Missense_Mutation_p.V151I	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	168					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				CAACGCCTACGTCACTGACGA	0.537													G|||	2	0.000399361	0.0	0.0014	5008	,	,		12023	0.0		0.001	False		,,,				2504	0.0				p.V168I		Atlas-SNP	.											.	BPHL	32	.	0			c.G502A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	109.0	84.0	93.0		502	4.4	0.7	6	dbSNP_132	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	BPHL	NM_004332.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	168/292	3129402	2,13004	2203	4300	6503	SO:0001583	missense	670	exon4			GCCTACGTCACTG	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.502G>A	6.37:g.3129402G>A	ENSP00000369739:p.Val168Ile	55.0	0.0	0		71.0	25.0	0.352113	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.973	0.973452	0.18736	0.0	2.33E-4	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380368;ENST00000380379	T;T;T;T	0.75704	-0.96;-0.96;-0.25;-0.96	5.23	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	N	0.25094	0.71	0.80722	D	1	B;B	0.13145	0.007;0.006	B;B	0.21917	0.037;0.022	T	0.30327	-0.9982	10	0.08837	T	0.75	-24.7051	10.9534	0.47343	0.1506:0.0:0.8494:0.0	.	168;151	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	I	151;151;151;168	ENSP00000390472:V151I;ENSP00000369734:V151I;ENSP00000369726:V151I;ENSP00000369739:V168I	ENSP00000369726:V151I	V	+	1	0	BPHL	3074401	1.000000	0.71417	0.747000	0.31113	0.384000	0.30261	6.156000	0.71840	1.206000	0.43276	0.561000	0.74099	GTC	G|1.000;A|0.000	0.000	strong		0.537	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
RABEP2	79874	hgsc.bcm.edu	37	16	28925694	28925694	+	Missense_Mutation	SNP	G	G	A	rs200278634		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28925694G>A	ENST00000358201.4	-	5	1345	c.757C>T	c.(757-759)Cgc>Tgc	p.R253C	RABEP2_ENST00000561803.1_5'Flank|RABEP2_ENST00000357573.6_Missense_Mutation_p.R253C|RABEP2_ENST00000544477.1_Missense_Mutation_p.R182C	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	253					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						AGGCCCTGGCGGCTTTGGGGC	0.667																																					p.R253C	Pancreas(66;639 1284 10093 31061 49099)	Atlas-SNP	.											.	RABEP2	48	.	0			c.C757T						PASS	.																																			SO:0001583	missense	79874	exon5			CCTGGCGGCTTTG	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.757C>T	16.37:g.28925694G>A	ENSP00000350934:p.Arg253Cys	116.0	0.0	0		112.0	57.0	0.508929	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836981	0.91117	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.49139	0.81;0.79;0.83	5.27	5.27	0.74061	.	0.417922	0.25375	N	0.031122	T	0.50905	0.1643	N	0.22421	0.69	0.41436	D	0.987899	D;D;D;D	0.76494	0.998;0.997;0.996;0.999	P;P;P;P	0.57846	0.761;0.648;0.761;0.828	T	0.55774	-0.8088	10	0.66056	D	0.02	-7.4463	15.8139	0.78583	0.0:0.0:1.0:0.0	.	182;253;253;253	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	C	253;253;182	ENSP00000350934:R253C;ENSP00000350186:R253C;ENSP00000442798:R182C	ENSP00000350186:R253C	R	-	1	0	RABEP2	28833195	0.267000	0.24122	0.974000	0.42286	0.900000	0.52787	3.127000	0.50484	2.457000	0.83068	0.462000	0.41574	CGC	.	.	weak		0.667	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816	
FBXO39	162517	hgsc.bcm.edu	37	17	6684003	6684003	+	Silent	SNP	C	C	G	rs17731806	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6684003C>G	ENST00000321535.4	+	2	946	c.816C>G	c.(814-816)tcC>tcG	p.S272S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	272										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						GGGGTATGTCCTGGGCCAAGC	0.542													C|||	120	0.0239617	0.0023	0.0216	5008	,	,		21815	0.0		0.0447	False		,,,				2504	0.0583				p.S272S		Atlas-SNP	.											.	FBXO39	50	.	0			c.C816G						PASS	.	C		63,4343	59.3+/-96.0	0,63,2140	75.0	63.0	67.0		816	0.6	1.0	17	dbSNP_123	67	472,8128	139.8+/-196.4	16,440,3844	no	coding-synonymous	FBXO39	NM_153230.2		16,503,5984	GG,GC,CC		5.4884,1.4299,4.1135		272/443	6684003	535,12471	2203	4300	6503	SO:0001819	synonymous_variant	162517	exon2			TATGTCCTGGGCC	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.816C>G	17.37:g.6684003C>G		42.0	0.0	0		49.0	28.0	0.571429	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																			C|0.963;G|0.037	0.037	strong		0.542	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
PON1	5444	hgsc.bcm.edu	37	7	94953765	94953765	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:94953765G>C	ENST00000222381.3	-	1	254	c.23C>G	c.(22-24)aCc>aGc	p.T8S	PON1_ENST00000542556.1_Intron	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	8					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CCCCAAGAGGGTGAGCGCAAT	0.612																																					p.T8S	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.C23G						PASS	.						137.0	100.0	113.0					7																	94953765		2203	4300	6503	SO:0001583	missense	5444	exon1			AAGAGGGTGAGCG	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.23C>G	7.37:g.94953765G>C	ENSP00000222381:p.Thr8Ser	36.0	0.0	0		48.0	14.0	0.291667	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.181847	0.01633	.	.	ENSG00000005421	ENST00000222381	T	0.34859	1.34	4.31	3.43	0.39272	Six-bladed beta-propeller, TolB-like (1);	0.403795	0.27000	N	0.021422	T	0.20780	0.0500	L	0.28014	0.82	0.40848	D	0.983722	B	0.02656	0.0	B	0.04013	0.001	T	0.06075	-1.0847	10	0.10902	T	0.67	-2.7887	8.2699	0.31838	0.106:0.0:0.894:0.0	.	8	P27169	PON1_HUMAN	S	8	ENSP00000222381:T8S	ENSP00000222381:T8S	T	-	2	0	PON1	94791701	0.991000	0.36638	0.488000	0.27440	0.038000	0.13279	2.607000	0.46300	1.414000	0.47017	0.555000	0.69702	ACC	.	.	none		0.612	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
EEFSEC	60678	hgsc.bcm.edu	37	3	128060346	128060346	+	Missense_Mutation	SNP	C	C	T	rs374389896		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128060346C>T	ENST00000254730.6	+	5	1111	c.1057C>T	c.(1057-1059)Cct>Tct	p.P353S	EEFSEC_ENST00000483457.1_Missense_Mutation_p.P298S|EEFSEC_ENST00000483569.1_3'UTR	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	353					selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						GTTCTTCAGTCCTGCTCCAGA	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		20430	0.0		0.0	False		,,,				2504	0.001				p.P353S		Atlas-SNP	.											.	EEFSEC	53	.	0			c.C1057T						PASS	.	C	SER/PRO	0,4406		0,0,2203	67.0	65.0	66.0		1057	5.4	1.0	3		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	EEFSEC	NM_021937.3	74	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	353/597	128060346	1,13005	2203	4300	6503	SO:0001583	missense	60678	exon5			TTCAGTCCTGCTC		CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"""elongation factor for selenoprotein translation"""	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.1057C>T	3.37:g.128060346C>T	ENSP00000254730:p.Pro353Ser	122.0	0.0	0		95.0	52.0	0.547368	NM_021937	Q96HZ6	Missense_Mutation	SNP	ENST00000254730.6	37	CCDS33849.1	.	.	.	.	.	.	.	.	.	.	C	9.164	1.019497	0.19355	0.0	1.16E-4	ENSG00000132394	ENST00000254730;ENST00000483457	T;T	0.53206	1.04;0.63	5.44	5.44	0.79542	.	0.098967	0.64402	D	0.000001	T	0.37732	0.1014	L	0.38531	1.155	0.45554	D	0.998502	B;B	0.23442	0.085;0.002	B;B	0.14023	0.01;0.003	T	0.28713	-1.0035	10	0.07325	T	0.83	-17.2308	19.2453	0.93899	0.0:1.0:0.0:0.0	.	298;353	C9J8T0;P57772	.;SELB_HUMAN	S	353;298	ENSP00000254730:P353S;ENSP00000417660:P298S	ENSP00000254730:P353S	P	+	1	0	EEFSEC	129543036	1.000000	0.71417	0.994000	0.49952	0.548000	0.35241	3.159000	0.50731	2.536000	0.85505	0.591000	0.81541	CCT	.	.	weak		0.493	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937	
PTPRD	5789	hgsc.bcm.edu	37	9	8376067	8376067	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:8376067T>G	ENST00000381196.4	-	36	5073	c.4530A>C	c.(4528-4530)gaA>gaC	p.E1510D	PTPRD_ENST00000540109.1_Missense_Mutation_p.E1510D|PTPRD_ENST00000356435.5_Missense_Mutation_p.E1510D|PTPRD_ENST00000486161.1_Missense_Mutation_p.E1103D|PTPRD_ENST00000358503.5_Missense_Mutation_p.E1488D|PTPRD_ENST00000355233.5_Missense_Mutation_p.E1104D|PTPRD_ENST00000397606.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000360074.4_Missense_Mutation_p.E1497D|PTPRD_ENST00000397617.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000397611.3_Missense_Mutation_p.E1100D|PTPRD_ENST00000537002.1_Missense_Mutation_p.E1100D	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1510	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ATTGTCTCACTTCTCTCTTCT	0.433										TSP Lung(15;0.13)																											p.E1510D		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A4530C						PASS	.						104.0	92.0	96.0					9																	8376067		2203	4299	6502	SO:0001583	missense	5789	exon39			TCTCACTTCTCTC	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4530A>C	9.37:g.8376067T>G	ENSP00000370593:p.Glu1510Asp	75.0	0.0	0		56.0	5.0	0.0892857	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.719582	0.48728	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.71	4.56	0.56223	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	M	0.76433	2.335	0.80722	D	1	B;P;P;P;B;P;B;P;B	0.43826	0.071;0.73;0.73;0.73;0.014;0.721;0.063;0.818;0.013	B;P;P;P;B;B;B;B;B	0.55087	0.036;0.768;0.768;0.768;0.03;0.203;0.035;0.255;0.024	T	0.45366	-0.9266	9	.	.	.	.	11.8465	0.52387	0.0:0.0696:0.0:0.9303	.	1103;1094;1103;1104;1100;1100;1497;1510;1510	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	D	1510;1510;1497;1488;1104;1103;1100;1100;981;1510;1103;1103	ENSP00000370593:E1510D;ENSP00000348812:E1510D;ENSP00000353187:E1497D;ENSP00000351293:E1488D;ENSP00000347373:E1104D;ENSP00000380741:E1103D;ENSP00000380735:E1100D;ENSP00000440515:E1100D;ENSP00000438164:E1510D;ENSP00000417093:E1103D;ENSP00000380731:E1103D	.	E	-	3	2	PTPRD	8366067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.262000	0.51538	2.178000	0.69098	0.477000	0.44152	GAA	.	.	none		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
SECISBP2	79048	hgsc.bcm.edu	37	9	91954848	91954848	+	Missense_Mutation	SNP	C	C	G	rs45452691	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91954848C>G	ENST00000375807.3	+	9	1353	c.1282C>G	c.(1282-1284)Caa>Gaa	p.Q428E	SECISBP2_ENST00000339901.4_Missense_Mutation_p.Q355E|SECISBP2_ENST00000534113.2_Missense_Mutation_p.Q360E	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	428			Q -> E (in dbSNP:rs45452691).		translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						ACCGAAATTTCAATCTAAGCA	0.408													C|||	90	0.0179712	0.0023	0.0202	5008	,	,		13904	0.0		0.0596	False		,,,				2504	0.0133				p.Q428E		Atlas-SNP	.											.	SECISBP2	64	.	0			c.C1282G						PASS	.	C	GLU/GLN	46,4360	47.5+/-82.1	0,46,2157	85.0	86.0	85.0		1282	3.7	0.7	9	dbSNP_127	85	507,8093	143.9+/-199.8	11,485,3804	no	missense	SECISBP2	NM_024077.3	29	11,531,5961	GG,GC,CC		5.8953,1.044,4.2519	benign	428/855	91954848	553,12453	2203	4300	6503	SO:0001583	missense	79048	exon9			AAATTTCAATCTA	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.1282C>G	9.37:g.91954848C>G	ENSP00000364965:p.Gln428Glu	61.0	0.0	0		43.0	19.0	0.44186	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	61	0.027930402930402932	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	49	0.06464379947229551	C	13.48	2.248565	0.39797	0.01044	0.058953	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113;ENST00000425851	T;T;T;T	0.72942	-0.68;-0.7;-0.69;0.94	4.64	3.73	0.42828	.	0.820878	0.10928	N	0.618701	T	0.13114	0.0318	L	0.51422	1.61	0.22571	N	0.998972	B;B;B	0.32467	0.255;0.372;0.255	B;B;B	0.33392	0.078;0.163;0.057	T	0.47328	-0.9126	10	0.02654	T	1	-0.1047	6.3816	0.21538	0.0:0.8236:0.0:0.1764	rs45452691;rs61744906	435;355;428	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	E	428;434;355;360;225	ENSP00000364965:Q428E;ENSP00000364959:Q355E;ENSP00000436650:Q360E;ENSP00000414288:Q225E	ENSP00000364959:Q355E	Q	+	1	0	SECISBP2	91144668	0.384000	0.25164	0.714000	0.30535	0.944000	0.59088	-0.422000	0.07043	2.583000	0.87209	0.655000	0.94253	CAA	C|0.961;G|0.039	0.039	strong		0.408	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077	
PCDHA13	56136	hgsc.bcm.edu	37	5	140263210	140263210	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140263210C>G	ENST00000289272.2	+	1	1357	c.1357C>G	c.(1357-1359)Ccg>Gcg	p.P453A	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.P453A|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	453	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGACAACGCGCCGGCGTTCGC	0.672																																					p.P453A	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,NS,carcinoma,-2,1	PCDHA13	213	1	0			c.C1357G						PASS	.						69.0	73.0	72.0					5																	140263210		2203	4299	6502	SO:0001583	missense	56136	exon1			AACGCGCCGGCGT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1357C>G	5.37:g.140263210C>G	ENSP00000289272:p.Pro453Ala	75.0	0.0	0		72.0	6.0	0.0833333	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388941	0.82902	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	D;D	0.84660	-1.88;-1.88	5.15	5.15	0.70609	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96046	0.8712	H	0.99299	4.505	0.49051	D	0.999749	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.994;0.989;0.995	D	0.98200	1.0467	9	0.87932	D	0	.	18.2655	0.90051	0.0:1.0:0.0:0.0	.	453;453;453	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	A	453	ENSP00000386821:P453A;ENSP00000289272:P453A	ENSP00000289272:P453A	P	+	1	0	PCDHA13	140243394	1.000000	0.71417	0.995000	0.50966	0.967000	0.64934	5.813000	0.69201	2.386000	0.81285	0.556000	0.70494	CCG	.	.	none		0.672	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
HORMAD2	150280	hgsc.bcm.edu	37	22	30518155	30518155	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30518155C>T	ENST00000336726.6	+	10	1126	c.771C>T	c.(769-771)atC>atT	p.I257I	HORMAD2_ENST00000403975.1_Silent_p.I257I	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	257					meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			CTACTGAGATCGCCCATCAGG	0.408																																					p.I257I		Atlas-SNP	.											.	HORMAD2	12	.	0			c.C771T						PASS	.						51.0	51.0	51.0					22																	30518155		1918	4128	6046	SO:0001819	synonymous_variant	150280	exon10			TGAGATCGCCCAT	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.771C>T	22.37:g.30518155C>T		106.0	0.0	0		107.0	52.0	0.485981	NM_152510	B5MEB2|Q8NHR2	Silent	SNP	ENST00000336726.6	37	CCDS46683.1																																																																																			.	.	none		0.408	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510	
CIT	11113	hgsc.bcm.edu	37	12	120222830	120222830	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120222830G>A	ENST00000261833.7	-	11	1387	c.1335C>T	c.(1333-1335)agC>agT	p.S445S	CIT_ENST00000392521.2_Silent_p.S445S|CIT_ENST00000537607.1_5'Flank	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	445					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TTTCCATGGAGCTAGTCTTGG	0.507																																					p.S445S		Atlas-SNP	.											.	CIT	535	.	0			c.C1335T						PASS	.						116.0	101.0	106.0					12																	120222830		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon11			CATGGAGCTAGTC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1335C>T	12.37:g.120222830G>A		107.0	0.0	0		91.0	25.0	0.274725	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	6.186	0.402510	0.11696	.	.	ENSG00000122966	ENST00000392520	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.76919	0.4055	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74228	-0.3733	4	.	.	.	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	.	.	.	V	73	.	.	A	-	2	0	CIT	118707213	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.810000	0.75216	2.779000	0.95612	0.655000	0.94253	GCT	.	.	none		0.507	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
C7orf72	100130988	hgsc.bcm.edu	37	7	50175760	50175760	+	Splice_Site	SNP	T	T	G	rs149326344	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:50175760T>G	ENST00000297001.6	+	5	984	c.934T>G	c.(934-936)Ttt>Gtt	p.F312V		NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	312										NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						ACCAATTAATTTGTAAGTTTT	0.373													T|||	11	0.00219649	0.0	0.0072	5008	,	,		20802	0.0		0.005	False		,,,				2504	0.001				p.F312V		Atlas-SNP	.											.	C7orf72	26	.	0			c.T934G						PASS	.	T	VAL/PHE	0,1384		0,0,692	310.0	268.0	281.0		934	5.7	1.0	7	dbSNP_134	281	12,3170		0,12,1579	yes	missense-near-splice	C7orf72	NM_001161834.2	50	0,12,2271	GG,GT,TT		0.3771,0.0,0.2628	benign	312/439	50175760	12,4554	692	1591	2283	SO:0001630	splice_region_variant	100130988	exon5			ATTAATTTGTAAG		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.935+1T>G	7.37:g.50175760T>G		177.0	0.0	0		114.0	28.0	0.245614	NM_001161834	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	37	CCDS47585.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	12.52	1.962444	0.34659	0.0	0.003771	ENSG00000164500	ENST00000297001	.	.	.	5.71	5.71	0.89125	.	0.332660	0.27323	N	0.019888	T	0.68961	0.3058	L	0.48642	1.525	0.38098	D	0.937182	D	0.76494	0.999	D	0.80764	0.994	T	0.74237	-0.3730	9	0.87932	D	0	.	12.382	0.55311	0.0:0.0:0.0:1.0	.	312	A4D263	CG072_HUMAN	V	312	.	ENSP00000297001:F312V	F	+	1	0	C7orf72	50146306	1.000000	0.71417	0.974000	0.42286	0.276000	0.26787	4.031000	0.57267	2.172000	0.68678	0.523000	0.50628	TTT	T|0.999;G|0.001	0.001	strong		0.373	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	Missense_Mutation
WDR90	197335	hgsc.bcm.edu	37	16	705344	705344	+	Silent	SNP	C	C	A	rs144704309	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:705344C>A	ENST00000293879.4	+	15	1594	c.1594C>A	c.(1594-1596)Cgg>Agg	p.R532R	WDR90_ENST00000549091.1_Silent_p.R532R|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	532										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GCGGCTCTGGCGGCTGCGTGG	0.701													C|||	3	0.000599042	0.0008	0.0	5008	,	,		15736	0.0		0.002	False		,,,				2504	0.0				p.R532R		Atlas-SNP	.											.	WDR90	107	.	0			c.C1594A						PASS	.	C		0,4352		0,0,2176	18.0	28.0	25.0		1594	3.6	1.0	16	dbSNP_134	25	19,8539		0,19,4260	no	coding-synonymous	WDR90	NM_145294.4		0,19,6436	AA,AC,CC		0.222,0.0,0.1472		532/1749	705344	19,12891	2176	4279	6455	SO:0001819	synonymous_variant	197335	exon15			CTCTGGCGGCTGC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.1594C>A	16.37:g.705344C>A		21.0	0.0	0		26.0	14.0	0.538462	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			C|0.999;A|0.001	0.001	strong		0.701	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
ACTG1	71	hgsc.bcm.edu	37	17	79479099	79479099	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479099G>T	ENST00000575842.1	-	2	619	c.193C>A	c.(193-195)Ctg>Atg	p.L65M	ACTG1_ENST00000331925.2_Missense_Mutation_p.L65M|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.L65M|ACTG1_ENST00000575087.1_Missense_Mutation_p.L65M|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	65					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			TTCAGGGTCAGGATGCCACGC	0.642																																					p.L65M		Atlas-SNP	.											.	ACTG1	55	.	0			c.C193A						PASS	.						71.0	69.0	69.0					17																	79479099		2203	4300	6503	SO:0001583	missense	71	exon3			GGGTCAGGATGCC		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.193C>A	17.37:g.79479099G>T	ENSP00000458162:p.Leu65Met	74.0	0.0	0		37.0	10.0	0.27027	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	G	7.842	0.722186	0.15372	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.94723	-3.5	3.99	1.97	0.26223	.	0.000000	0.52532	U	0.000061	D	0.97356	0.9135	M	0.91663	3.23	0.41069	D	0.985436	D	0.61697	0.99	D	0.83275	0.996	D	0.96801	0.9589	10	0.87932	D	0	.	11.7241	0.51700	0.1712:0.0:0.8288:0.0	.	65	P63261	ACTG_HUMAN	M	65	ENSP00000331514:L65M	ENSP00000331514:L65M	L	-	1	2	ACTG1	77093694	1.000000	0.71417	0.992000	0.48379	0.176000	0.22953	7.295000	0.78780	0.055000	0.16094	-1.119000	0.02030	CTG	.	.	none		0.642	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	
TMEM108	66000	hgsc.bcm.edu	37	3	133098806	133098806	+	Missense_Mutation	SNP	C	C	T	rs34111099	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133098806C>T	ENST00000321871.6	+	4	461	c.251C>T	c.(250-252)cCg>cTg	p.P84L	TMEM108_ENST00000515826.1_Missense_Mutation_p.P84L|TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000393130.3_Missense_Mutation_p.P84L	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	84	Pro-rich.		P -> L (in dbSNP:rs34111099). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12975309}.			integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ATGGCAACACCGACACCCCGT	0.627													c|||	145	0.0289537	0.0136	0.0173	5008	,	,		15503	0.0		0.0616	False		,,,				2504	0.0542				p.P84L		Atlas-SNP	.											TMEM108,rectum,carcinoma,0,1	TMEM108	67	1	0			c.C251T						PASS	.		LEU/PRO,LEU/PRO	82,4324	68.7+/-106.4	2,78,2123	97.0	89.0	92.0		251,251	0.9	0.0	3	dbSNP_126	92	597,8003	157.7+/-211.4	23,551,3726	yes	missense,missense	TMEM108	NM_001136469.1,NM_023943.2	98,98	25,629,5849	TT,TC,CC		6.9419,1.8611,5.2207	benign,benign	84/576,84/576	133098806	679,12327	2203	4300	6503	SO:0001583	missense	66000	exon4			CAACACCGACACC	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"""cancer/testis antigen 124"""					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.251C>T	3.37:g.133098806C>T	ENSP00000324651:p.Pro84Leu	125.0	0.0	0		109.0	55.0	0.504587	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	61	0.027930402930402932	12	0.024390243902439025	4	0.011049723756906077	0	0.0	45	0.059366754617414245	c	2.305	-0.359279	0.05138	0.018611	0.069419	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000514894;ENST00000512662;ENST00000512137;ENST00000515826;ENST00000510183	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	2.76	0.893	0.19236	.	0.467395	0.15982	N	0.235273	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B;B	0.29862	0.259;0.007	B;B	0.20384	0.029;0.004	T	0.08269	-1.0730	10	0.52906	T	0.07	0.0198	3.2014	0.06651	0.2607:0.5932:0.0:0.1461	rs34111099	84;84	E9PB58;Q6UXF1	.;TM108_HUMAN	L	84;84;35;35;84;84;84	ENSP00000324651:P84L;ENSP00000376838:P84L;ENSP00000422072:P35L;ENSP00000427447:P35L;ENSP00000426301:P84L;ENSP00000423338:P84L;ENSP00000421486:P84L	ENSP00000324651:P84L	P	+	2	0	TMEM108	134581496	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.106000	0.15354	0.219000	0.20840	0.457000	0.33378	CCG	C|0.952;T|0.048	0.048	strong		0.627	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943	
NEFM	4741	hgsc.bcm.edu	37	8	24774646	24774646	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:24774646C>G	ENST00000221166.5	+	3	2060	c.1278C>G	c.(1276-1278)caC>caG	p.H426Q	GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000437366.2_Missense_Mutation_p.H426Q|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000518131.1_Missense_Mutation_p.H426Q|NEFM_ENST00000433454.2_Missense_Mutation_p.H50Q			P07197	NFM_HUMAN	neurofilament, medium polypeptide	426	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TGTATACACACCGACCCCCAA	0.443																																					p.H426Q		Atlas-SNP	.											.	NEFM	115	.	0			c.C1278G						PASS	.						65.0	64.0	65.0					8																	24774646		2203	4300	6503	SO:0001583	missense	4741	exon3			TACACACCGACCC	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.1278C>G	8.37:g.24774646C>G	ENSP00000221166:p.His426Gln	148.0	0.0	0		140.0	79.0	0.564286	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	37	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559906	0.45590	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366;ENST00000433454	D;D;D;D	0.93659	-1.61;-1.62;-1.64;-3.26	4.92	4.92	0.64577	.	0.128053	0.34531	N	0.003893	D	0.92932	0.7751	L	0.56124	1.755	0.58432	D	0.99999	D;P	0.54047	0.964;0.947	P;B	0.46275	0.51;0.355	D	0.93719	0.7031	10	0.62326	D	0.03	.	18.4956	0.90864	0.0:1.0:0.0:0.0	.	426;426	E7EMV2;P07197	.;NFM_HUMAN	Q	426;426;426;50	ENSP00000221166:H426Q;ENSP00000427872:H426Q;ENSP00000410137:H426Q;ENSP00000412295:H50Q	ENSP00000221166:H426Q	H	+	3	2	NEFM	24830551	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	2.443000	0.44881	2.421000	0.82119	0.563000	0.77884	CAC	.	.	none		0.443	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382	
DOCK8	81704	hgsc.bcm.edu	37	9	399255	399255	+	Missense_Mutation	SNP	G	G	A	rs34627722	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:399255G>A	ENST00000453981.1	+	26	3342	c.3230G>A	c.(3229-3231)aGc>aAc	p.S1077N	DOCK8_ENST00000382329.1_Missense_Mutation_p.S544N|DOCK8_ENST00000432829.2_Missense_Mutation_p.S1009N|DOCK8_ENST00000382331.1_Missense_Mutation_p.S379N|DOCK8_ENST00000469391.1_Missense_Mutation_p.S977N			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1077					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CATTATTGCAGCCAGGTGAGT	0.512													A|||	306	0.0611022	0.1415	0.0865	5008	,	,		14936	0.0		0.0338	False		,,,				2504	0.0256				p.S1077N		Atlas-SNP	.											.	DOCK8	401	.	0			c.G3230A						PASS	.	A	ASN/SER,ASN/SER,ASN/SER	473,3933	779.0+/-414.3	27,419,1757	139.0	127.0	131.0		2930,3026,3230	3.7	1.0	9	dbSNP_126	131	281,8319	805.8+/-407.3	4,273,4023	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	46,46,46	31,692,5780	AA,AG,GG		3.2674,10.7354,5.7973	benign,benign,benign	977/2000,1009/2032,1077/2100	399255	754,12252	2203	4300	6503	SO:0001583	missense	81704	exon26			ATTGCAGCCAGGT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.3230G>A	9.37:g.399255G>A	ENSP00000408464:p.Ser1077Asn	138.0	0.0	0		96.0	40.0	0.416667	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	126	0.057692307692307696	69	0.1402439024390244	28	0.07734806629834254	0	0.0	29	0.03825857519788918	A	12.92	2.081509	0.36758	0.107354	0.032674	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382331;ENST00000382329	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	6.04	3.69	0.42338	.	0.254353	0.44483	N	0.000448	T	0.00073	0.0002	N	0.04994	-0.135	0.20563	N	0.999885	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.41662	-0.9496	10	0.18276	T	0.48	.	7.2832	0.26322	0.7505:0.1227:0.1269:0.0	rs34627722;rs57242371	379;977;544;1077	A2A370;E9PH09;A2A369;Q8NF50	.;.;.;DOCK8_HUMAN	N	1077;1045;1009;977;379;544	ENSP00000408464:S1077N;ENSP00000394888:S1009N;ENSP00000419438:S977N;ENSP00000371768:S379N;ENSP00000371766:S544N	ENSP00000287364:S1045N	S	+	2	0	DOCK8	389255	1.000000	0.71417	0.993000	0.49108	0.891000	0.51852	4.343000	0.59348	0.173000	0.19788	-0.360000	0.07572	AGC	G|0.945;A|0.055	0.055	strong		0.512	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
FGF5	2250	hgsc.bcm.edu	37	4	81188221	81188221	+	Missense_Mutation	SNP	G	G	T	rs112475347		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:81188221G>T	ENST00000312465.7	+	1	469	c.243G>T	c.(241-243)tgG>tgT	p.W81C	FGF5_ENST00000456523.3_Missense_Mutation_p.W81C	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	81					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						GTTTCCAGTGGAGCCCCTCGG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		14528	0.0		0.001	False		,,,				2504	0.0				p.W81C		Atlas-SNP	.											.	FGF5	49	.	0			c.G243T						PASS	.	G	CYS/TRP,CYS/TRP	1,4405	2.1+/-5.4	0,1,2202	50.0	57.0	55.0		243,243	5.4	1.0	4	dbSNP_132	55	20,8580	14.6+/-50.1	0,20,4280	yes	missense,missense	FGF5	NM_004464.3,NM_033143.2	215,215	0,21,6482	TT,TG,GG		0.2326,0.0227,0.1615	probably-damaging,probably-damaging	81/269,81/124	81188221	21,12985	2203	4300	6503	SO:0001583	missense	2250	exon1			CCAGTGGAGCCCC	M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675		"""Endogenous ligands"""	3683	protein-coding gene	gene with protein product		165190				3211147, 2577873	Standard	NM_001291812		Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.243G>T	4.37:g.81188221G>T	ENSP00000311697:p.Trp81Cys	121.0	0.0	0		111.0	57.0	0.513514	NM_004464	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	37	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410863	0.83340	2.27E-4	0.002326	ENSG00000138675	ENST00000312465;ENST00000456523	T;T	0.08102	3.13;3.13	5.41	5.41	0.78517	.	0.695962	0.12612	N	0.453741	T	0.22003	0.0530	L	0.36672	1.1	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.65874	0.939;0.72	T	0.00837	-1.1546	10	0.46703	T	0.11	.	19.0018	0.92837	0.0:0.0:1.0:0.0	.	81;81	P12034-2;P12034	.;FGF5_HUMAN	C	81	ENSP00000311697:W81C;ENSP00000398353:W81C	ENSP00000311697:W81C	W	+	3	0	FGF5	81407245	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.324000	0.72896	2.816000	0.96949	0.561000	0.74099	TGG	G|0.998;T|0.002	0.002	strong		0.607	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2		
FEZ2	9637	hgsc.bcm.edu	37	2	36818109	36818109	+	Silent	SNP	T	T	C	rs117617575	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:36818109T>C	ENST00000405912.3	-	2	311	c.312A>G	c.(310-312)gtA>gtG	p.V104V	FEZ2_ENST00000305852.7_5'UTR|FEZ2_ENST00000379245.4_Silent_p.V104V	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	104					axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165)					breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	7		all_hematologic(82;0.21)				ACTTCCAGTCTACAGGCATCA	0.368													T|||	3	0.000599042	0.0008	0.0	5008	,	,		21313	0.001		0.001	False		,,,				2504	0.0				p.V104V		Atlas-SNP	.											.	FEZ2	13	.	0			c.A312G						PASS	.	T	,	3,3759		0,3,1878	125.0	113.0	117.0		312,312	-9.1	1.0	2	dbSNP_132	117	41,8165		0,41,4062	no	coding-synonymous,coding-synonymous	FEZ2	NM_001042548.1,NM_005102.2	,	0,44,5940	CC,CT,TT		0.4996,0.0797,0.3676	,	104/381,104/354	36818109	44,11924	1881	4103	5984	SO:0001819	synonymous_variant	9637	exon2			CCAGTCTACAGGC	U60061	CCDS46257.1, CCDS46258.1	2p21	2008-05-15			ENSG00000171055	ENSG00000171055			3660	protein-coding gene	gene with protein product		604826				9096408	Standard	NM_005102		Approved		uc002rpg.2	Q9UHY8	OTTHUMG00000152148	ENST00000405912.3:c.312A>G	2.37:g.36818109T>C		176.0	0.0	0		197.0	92.0	0.467005	NM_001042548	Q5EBN3|Q76LN0|Q99690	Silent	SNP	ENST00000405912.3	37	CCDS46257.1																																																																																			T|0.998;C|0.002	0.002	strong		0.368	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1		
OR2C1	4993	hgsc.bcm.edu	37	16	3406651	3406651	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3406651G>A	ENST00000304936.2	+	1	763	c.711G>A	c.(709-711)gcG>gcA	p.A237A		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	237					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GGCGAAAGGCGTTCAATACGT	0.547																																					p.A237A		Atlas-SNP	.											.	OR2C1	38	.	0			c.G711A						PASS	.						148.0	122.0	131.0					16																	3406651		2197	4300	6497	SO:0001819	synonymous_variant	4993	exon1			AAAGGCGTTCAAT	AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"""GPCR / Class A : Olfactory receptors"""	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.711G>A	16.37:g.3406651G>A		67.0	0.0	0		81.0	34.0	0.419753	NM_012368	A0AVA4|Q6IF34|Q6IF55	Silent	SNP	ENST00000304936.2	37	CCDS10502.1																																																																																			.	.	none		0.547	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
SPATA16	83893	hgsc.bcm.edu	37	3	172835469	172835469	+	Missense_Mutation	SNP	T	T	C	rs115897458	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:172835469T>C	ENST00000351008.3	-	2	236	c.53A>G	c.(52-54)cAt>cGt	p.H18R		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	18					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			AAGCTGATCATGATAGATCCT	0.428													T|||	7	0.00139776	0.0	0.0014	5008	,	,		19584	0.0		0.006	False		,,,				2504	0.0				p.H18R		Atlas-SNP	.											.	SPATA16	111	.	0			c.A53G						PASS	.	T	ARG/HIS	7,4399	14.3+/-33.2	0,7,2196	181.0	168.0	173.0		53	-1.2	0.0	3	dbSNP_132	173	65,8535	40.3+/-97.0	1,63,4236	yes	missense	SPATA16	NM_031955.5	29	1,70,6432	CC,CT,TT		0.7558,0.1589,0.5536	benign	18/570	172835469	72,12934	2203	4300	6503	SO:0001583	missense	83893	exon2			TGATCATGATAGA	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.53A>G	3.37:g.172835469T>C	ENSP00000341765:p.His18Arg	231.0	1.0	0.004329		210.0	92.0	0.438095	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	37	CCDS3221.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	0.017	-1.490377	0.01018	0.001589	0.007558	ENSG00000144962	ENST00000351008	T	0.14022	2.54	5.23	-1.2	0.09554	.	0.934285	0.08915	N	0.875252	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43048	-0.9415	10	0.06757	T	0.87	-2.7449	5.2779	0.15659	0.0:0.2885:0.3529:0.3586	.	18	Q9BXB7	SPT16_HUMAN	R	18	ENSP00000341765:H18R	ENSP00000341765:H18R	H	-	2	0	SPATA16	174318163	0.041000	0.20044	0.020000	0.16555	0.075000	0.17131	0.281000	0.18810	-0.144000	0.11314	0.528000	0.53228	CAT	T|0.996;C|0.004	0.004	strong		0.428	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
TTC30A	92104	hgsc.bcm.edu	37	2	178482246	178482246	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:178482246T>G	ENST00000355689.5	-	1	1448	c.1184A>C	c.(1183-1185)aAg>aCg	p.K395T	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	395					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			CTGTACTTGCTTGGTGAGTCT	0.453																																					p.K395T		Atlas-SNP	.											.	TTC30A	60	.	0			c.A1184C						PASS	.						238.0	237.0	237.0					2																	178482246		2203	4300	6503	SO:0001583	missense	92104	exon1			ACTTGCTTGGTGA	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.1184A>C	2.37:g.178482246T>G	ENSP00000347915:p.Lys395Thr	241.0	0.0	0		246.0	31.0	0.126016	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	.	.	.	.	.	.	.	.	.	.	T	3.347	-0.133430	0.06711	.	.	ENSG00000197557	ENST00000355689	T	0.21734	1.99	5.91	-6.04	0.02178	.	0.330531	0.38959	N	0.001515	T	0.29524	0.0736	M	0.85945	2.785	0.49798	D	0.999822	B	0.32918	0.39	B	0.39617	0.305	T	0.29761	-1.0001	10	0.46703	T	0.11	.	15.5572	0.76203	0.6891:0.0:0.0:0.3109	.	395	Q86WT1	TT30A_HUMAN	T	395	ENSP00000347915:K395T	ENSP00000347915:K395T	K	-	2	0	TTC30A	178190492	0.212000	0.23540	0.397000	0.26308	0.105000	0.19272	0.477000	0.22196	-1.344000	0.02216	-1.497000	0.00963	AAG	.	.	none		0.453	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
FAT4	79633	hgsc.bcm.edu	37	4	126329944	126329944	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:126329944A>T	ENST00000394329.3	+	4	5928	c.5915A>T	c.(5914-5916)gAt>gTt	p.D1972V	FAT4_ENST00000335110.5_Missense_Mutation_p.D270V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1972	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ACTGATGCAGATGATGGTATG	0.289																																					p.D1972V		Atlas-SNP	.											.	FAT4	1752	.	0			c.A5915T						PASS	.						95.0	96.0	96.0					4																	126329944		2203	4299	6502	SO:0001583	missense	79633	exon4			ATGCAGATGATGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5915A>T	4.37:g.126329944A>T	ENSP00000377862:p.Asp1972Val	78.0	0.0	0		62.0	4.0	0.0645161	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	21.0	4.077181	0.76415	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.74737	-0.87;-0.87	5.22	5.22	0.72569	Cadherin (4);Cadherin-like (1);	0.000000	0.35378	U	0.003259	D	0.91294	0.7255	H	0.98005	4.125	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.94437	0.7655	10	0.87932	D	0	.	15.12	0.72434	1.0:0.0:0.0:0.0	.	270;1972	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	1972;270	ENSP00000377862:D1972V;ENSP00000335169:D270V	ENSP00000335169:D270V	D	+	2	0	FAT4	126549394	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.770000	0.91746	1.971000	0.57363	0.528000	0.53228	GAT	.	.	none		0.289	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CEL	1056	hgsc.bcm.edu	37	9	135942008	135942008	+	Silent	SNP	C	C	T	rs529444912		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135942008C>T	ENST00000372080.4	+	5	655	c.639C>T	c.(637-639)ctC>ctT	p.L213L	CEL_ENST00000351304.7_Silent_p.L210L	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	210					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		ACATCACGCTCTTCGGGGAGT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14997	0.0		0.0	False		,,,				2504	0.0				p.L213L		Atlas-SNP	.											.	CEL	71	.	0			c.C639T						PASS	.						86.0	96.0	93.0					9																	135942008		1964	4160	6124	SO:0001819	synonymous_variant	1056	exon5			CACGCTCTTCGGG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.639C>T	9.37:g.135942008C>T		33.0	0.0	0		52.0	26.0	0.5	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	37	CCDS43896.1																																																																																			.	.	none		0.617	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
OR4A47	403253	hgsc.bcm.edu	37	11	48511105	48511105	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:48511105T>G	ENST00000446524.1	+	1	837	c.761T>G	c.(760-762)tTt>tGt	p.F254C		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						CCTTGTATTTTTATGTATGCT	0.428																																					p.F254C		Atlas-SNP	.											.	OR4A47	72	.	0			c.T761G						PASS	.						211.0	204.0	207.0					11																	48511105		2201	4298	6499	SO:0001583	missense	403253	exon1			GTATTTTTATGTA	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.761T>G	11.37:g.48511105T>G	ENSP00000412752:p.Phe254Cys	89.0	0.0	0		106.0	8.0	0.0754717	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	12.63	1.994217	0.35226	.	.	ENSG00000237388	ENST00000446524	T	0.00287	8.29	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000026	T	0.00412	0.0013	M	0.84773	2.715	0.39849	D	0.973213	P	0.39157	0.662	B	0.42112	0.376	T	0.71510	-0.4571	10	0.72032	D	0.01	.	11.9052	0.52708	0.0:0.0:0.0:1.0	.	254	Q6IF82	O4A47_HUMAN	C	254	ENSP00000412752:F254C	ENSP00000412752:F254C	F	+	2	0	OR4A47	48467681	0.290000	0.24343	1.000000	0.80357	0.291000	0.27294	2.135000	0.42112	1.692000	0.51112	0.172000	0.16884	TTT	.	.	none		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
AP1M1	8907	hgsc.bcm.edu	37	19	16318904	16318904	+	Silent	SNP	G	G	C	rs143435975	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:16318904G>C	ENST00000291439.3	+	4	791	c.342G>C	c.(340-342)ctG>ctC	p.L114L	AP1M1_ENST00000429941.2_Silent_p.L114L|AP1M1_ENST00000541844.1_Silent_p.L42L|AP1M1_ENST00000590756.1_Silent_p.L42L|AP1M1_ENST00000444449.2_Silent_p.L114L	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	114					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						ACGAGCTGCTGGACGAGCTCA	0.622													G|||	3	0.000599042	0.0	0.0	5008	,	,		16238	0.001		0.002	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	AP1M1	48	.	0			c.G342C						PASS	.	G	,	8,4398	14.3+/-33.2	0,8,2195	112.0	104.0	107.0		342,342	1.5	1.0	19	dbSNP_134	107	56,8544	34.8+/-89.0	0,56,4244	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	0,64,6439	CC,CG,GG		0.6512,0.1816,0.4921	,	114/436,114/424	16318904	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	8907	exon4			GCTGCTGGACGAG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.342G>C	19.37:g.16318904G>C		109.0	0.0	0		112.0	58.0	0.517857	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																			G|0.996;C|0.004	0.004	strong		0.622	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493	
FAT1	2195	hgsc.bcm.edu	37	4	187541971	187541971	+	Silent	SNP	G	G	A	rs372720339	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187541971G>A	ENST00000441802.2	-	10	5978	c.5769C>T	c.(5767-5769)atC>atT	p.I1923I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1923	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ACTTCTCCCCGATGTTGCCTT	0.438										HNSCC(5;0.00058)			G|||	2	0.000399361	0.0008	0.0	5008	,	,		20290	0.0		0.0	False		,,,				2504	0.001				p.I1923I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C5769T						PASS	.						92.0	94.0	93.0					4																	187541971		1917	4141	6058	SO:0001819	synonymous_variant	2195	exon10			CTCCCCGATGTTG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5769C>T	4.37:g.187541971G>A		135.0	0.0	0		119.0	62.0	0.521008	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			.	.	alt		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ESR1	2099	hgsc.bcm.edu	37	6	152201863	152201863	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152201863C>T	ENST00000206249.3	+	3	1079	c.717C>T	c.(715-717)gcC>gcT	p.A239A	ESR1_ENST00000440973.1_Silent_p.A239A|ESR1_ENST00000338799.5_Silent_p.A239A|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000427531.2_Silent_p.A66A|ESR1_ENST00000456483.2_Silent_p.A239A|ESR1_ENST00000443427.1_Silent_p.A239A	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	239	Mediates interaction with DNTTIP2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	GCTGCCAGGCCTGCCGGCTCC	0.527																																					p.A239A		Atlas-SNP	.											.	ESR1	94	.	0			c.C717T						PASS	.						54.0	55.0	54.0					6																	152201863		2203	4300	6503	SO:0001819	synonymous_variant	2099	exon3			CCAGGCCTGCCGG	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.717C>T	6.37:g.152201863C>T		59.0	0.0	0		50.0	4.0	0.08	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657168	0.29425	.	.	ENSG00000091831	ENST00000427531	.	.	.	5.42	4.54	0.55810	.	.	.	.	.	T	0.52273	0.1724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50725	-0.8794	4	.	.	.	.	11.7374	0.51773	0.0:0.8597:0.0:0.1403	.	.	.	.	L	144	.	.	P	+	2	0	ESR1	152243556	0.957000	0.32711	1.000000	0.80357	0.997000	0.91878	0.119000	0.15626	2.563000	0.86464	0.655000	0.94253	CCT	.	.	none		0.527	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
DHX57	90957	hgsc.bcm.edu	37	2	39090515	39090515	+	Missense_Mutation	SNP	T	T	G	rs199537184		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:39090515T>G	ENST00000295373.6	-	3	497	c.371A>C	c.(370-372)gAt>gCt	p.D124A	AC018693.6_ENST00000442829.1_RNA|DHX57_ENST00000479345.2_5'UTR	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	124							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				AGATCCAGCATCAGCATCTTG	0.398																																					p.D124A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A371C						PASS	.	T	ALA/ASP	0,4406		0,0,2203	119.0	116.0	117.0		371	5.7	1.0	2		117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DHX57	NM_198963.1	126	0,2,6501	GG,GT,TT		0.0233,0.0,0.0154	benign	124/1387	39090515	2,13004	2203	4300	6503	SO:0001583	missense	90957	exon3			CCAGCATCAGCAT	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.371A>C	2.37:g.39090515T>G	ENSP00000295373:p.Asp124Ala	46.0	0.0	0		58.0	30.0	0.517241	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443869	0.43429	0.0	2.33E-4	ENSG00000163214	ENST00000295373;ENST00000355320;ENST00000417233	T	0.02812	4.15	5.68	5.68	0.88126	.	0.107041	0.41294	D	0.000916	T	0.02380	0.0073	N	0.19112	0.55	0.41499	D	0.988279	B;B	0.28350	0.208;0.012	B;B	0.22152	0.038;0.006	T	0.60786	-0.7194	10	0.22706	T	0.39	.	12.2022	0.54333	0.0:0.0:0.1822:0.8178	.	124;124	Q6P158-2;Q6P158	.;DHX57_HUMAN	A	124;22;22	ENSP00000295373:D124A	ENSP00000295373:D124A	D	-	2	0	DHX57	38944019	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	5.043000	0.64208	2.156000	0.67533	0.459000	0.35465	GAT	.	.	weak		0.398	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
KIAA1143	57456	hgsc.bcm.edu	37	3	44794955	44794955	+	Missense_Mutation	SNP	T	T	C	rs138479225	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44794955T>C	ENST00000296121.4	-	3	402	c.343A>G	c.(343-345)Agc>Ggc	p.S115G	KIAA1143_ENST00000484437.1_5'UTR	NM_020696.3	NP_065747.1	Q96AT1	K1143_HUMAN	KIAA1143	115										NS(1)|breast(1)|central_nervous_system(1)|large_intestine(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00847)|KIRC - Kidney renal clear cell carcinoma(197;0.0465)|Kidney(197;0.0582)		TTTTTTGAGCTTGCTGTTAAA	0.358													T|||	7	0.00139776	0.0	0.0014	5008	,	,		16388	0.0		0.006	False		,,,				2504	0.0				p.S115G		Atlas-SNP	.											.	KIAA1143	10	.	0			c.A343G						PASS	.	T	GLY/SER	8,4398	14.3+/-33.2	0,8,2195	81.0	84.0	83.0		343	5.2	1.0	3	dbSNP_134	83	32,8562	22.8+/-68.1	0,32,4265	yes	missense	KIAA1143	NM_020696.3	56	0,40,6460	CC,CT,TT		0.3724,0.1816,0.3077	benign	115/155	44794955	40,12960	2203	4297	6500	SO:0001583	missense	57456	exon3			TTGAGCTTGCTGT	AB032969	CCDS2721.1	3p21.31	2005-08-15			ENSG00000163807	ENSG00000163807			29198	protein-coding gene	gene with protein product						10574461	Standard	NM_020696		Approved		uc011bac.2	Q96AT1	OTTHUMG00000133088	ENST00000296121.4:c.343A>G	3.37:g.44794955T>C	ENSP00000296121:p.Ser115Gly	110.0	0.0	0		140.0	72.0	0.514286	NM_020696	A8K0I4|Q96HJ8|Q9ULS7	Missense_Mutation	SNP	ENST00000296121.4	37	CCDS2721.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	18.36	3.606381	0.66445	0.001816	0.003724	ENSG00000163807	ENST00000296121	T	0.51325	0.71	5.17	5.17	0.71159	.	0.125552	0.64402	D	0.000001	T	0.38161	0.1030	M	0.68593	2.085	0.54753	D	0.999989	P	0.36909	0.573	B	0.33454	0.164	T	0.45948	-0.9226	10	0.44086	T	0.13	-11.295	14.9851	0.71342	0.0:0.0:0.0:1.0	.	115	Q96AT1	K1143_HUMAN	G	115	ENSP00000296121:S115G	ENSP00000296121:S115G	S	-	1	0	KIAA1143	44769959	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.531000	0.67148	2.074000	0.62210	0.377000	0.23210	AGC	T|0.997;C|0.003	0.003	strong		0.358	KIAA1143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256746.1	NM_020696	
ANKRD66	100287718	hgsc.bcm.edu	37	6	46721588	46721588	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:46721588C>T	ENST00000565422.1	+	4	463	c.458C>T	c.(457-459)gCa>gTa	p.A153V	ANKRD66_ENST00000536046.1_Missense_Mutation_p.A124V	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	153																	ACTCTCCATGCATTGCACGCT	0.517																																					p.A153V		Atlas-SNP	.											.	.	.	.	0			c.C458T						PASS	.						86.0	72.0	77.0					6																	46721588		692	1591	2283	SO:0001583	missense	100287718	exon4			TCCATGCATTGCA	AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.458C>T	6.37:g.46721588C>T	ENSP00000454770:p.Ala153Val	115.0	0.0	0		109.0	7.0	0.0642202	NM_001162435		Missense_Mutation	SNP	ENST00000565422.1	37	CCDS59024.1																																																																																			.	.	none		0.517	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1	NM_001162435	
GRIK2	2898	hgsc.bcm.edu	37	6	102074485	102074485	+	Missense_Mutation	SNP	G	G	A	rs201893729		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:102074485G>A	ENST00000421544.1	+	3	1004	c.514G>A	c.(514-516)Gtc>Atc	p.V172I	GRIK2_ENST00000358361.3_Missense_Mutation_p.V172I|GRIK2_ENST00000369138.1_Missense_Mutation_p.V172I|GRIK2_ENST00000413795.1_Missense_Mutation_p.V172I|GRIK2_ENST00000369137.3_Missense_Mutation_p.V172I|GRIK2_ENST00000369134.4_Missense_Mutation_p.V123I|GRIK2_ENST00000318991.6_Missense_Mutation_p.V172I	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	172					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GTGGAAAACCGTCACGGTTGT	0.408																																					p.V172I		Atlas-SNP	.											GRIK2_ENST00000421544,NS,carcinoma,0,2	GRIK2	487	2	0			c.G514A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	73.0	77.0	76.0		514,514,514	5.8	1.0	6		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	172/893,172/909,172/870	102074485	1,13005	2203	4300	6503	SO:0001583	missense	2898	exon3			AAAACCGTCACGG		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.514G>A	6.37:g.102074485G>A	ENSP00000397026:p.Val172Ile	96.0	0.0	0		107.0	60.0	0.560748	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278793	0.59758	0.0	1.16E-4	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076	D;D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.79	5.79	0.91817	Extracellular ligand-binding receptor (1);	0.135274	0.49305	D	0.000153	T	0.80788	0.4690	L	0.46670	1.46	0.51767	D	0.999939	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.21151	0.033;0.022;0.019	T	0.74928	-0.3497	10	0.45353	T	0.12	.	20.024	0.97514	0.0:0.0:1.0:0.0	.	172;172;172	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	I	172;172;172;172;172;172;172;123;134	ENSP00000397026:V172I;ENSP00000405596:V172I;ENSP00000358134:V172I;ENSP00000351128:V172I;ENSP00000358133:V172I;ENSP00000313276:V172I;ENSP00000358130:V123I	ENSP00000313276:V172I	V	+	1	0	GRIK2	102181178	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.647000	0.83462	2.718000	0.92993	0.655000	0.94253	GTC	G|0.999;A|0.001	0.001	weak		0.408	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
RNF123	63891	hgsc.bcm.edu	37	3	49749979	49749979	+	Missense_Mutation	SNP	C	C	T	rs201817210		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49749979C>T	ENST00000327697.6	+	27	2708	c.2564C>T	c.(2563-2565)aCa>aTa	p.T855I	RNF123_ENST00000432042.1_Missense_Mutation_p.T709I|RNF123_ENST00000433785.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	855					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GGTGATCGCACAGGGTCTCTC	0.582																																					p.T855I		Atlas-SNP	.											.	RNF123	100	.	0			c.C2564T						PASS	.						166.0	126.0	140.0					3																	49749979		2203	4300	6503	SO:0001583	missense	63891	exon27			ATCGCACAGGGTC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2564C>T	3.37:g.49749979C>T	ENSP00000328287:p.Thr855Ile	126.0	0.0	0		110.0	45.0	0.409091	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.038965	0.55003	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.76968	-0.74;-1.06	5.91	5.91	0.95273	.	0.088191	0.85682	D	0.000000	D	0.84570	0.5501	L	0.55481	1.735	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.60789	0.879;0.879	T	0.82831	-0.0263	10	0.41790	T	0.15	-16.3403	19.2739	0.94023	0.0:1.0:0.0:0.0	.	709;855	C9J266;Q5XPI4	.;RN123_HUMAN	I	855;855;709	ENSP00000328287:T855I;ENSP00000392443:T709I	ENSP00000328287:T855I	T	+	2	0	RNF123	49724983	1.000000	0.71417	0.966000	0.40874	0.279000	0.26890	4.573000	0.60893	2.803000	0.96430	0.650000	0.86243	ACA	C|0.999;T|0.001	0.001	weak		0.582	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
KCNMB3	27094	hgsc.bcm.edu	37	3	178962370	178962370	+	Silent	SNP	C	C	T	rs139532669	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:178962370C>T	ENST00000314235.5	-	3	883	c.372G>A	c.(370-372)ccG>ccA	p.P124P	KCNMB3_ENST00000497599.1_Silent_p.P122P|KCNMB3_ENST00000486944.1_5'Flank|KCNMB3_ENST00000349697.2_Silent_p.P122P|KCNMB3_ENST00000392685.2_Silent_p.P120P|KCNMB3_ENST00000485523.1_Silent_p.P102P	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	124					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	CCTGAAGACACGGGTACTTCC	0.498													C|||	7	0.00139776	0.0	0.0029	5008	,	,		17550	0.0		0.004	False		,,,				2504	0.001				p.P124P		Atlas-SNP	.											.	KCNMB3	46	.	0			c.G372A						PASS	.	C	,,,,	6,4400	11.4+/-27.6	0,6,2197	110.0	104.0	106.0		366,372,366,306,360	-10.8	0.4	3	dbSNP_134	106	77,8523	46.7+/-105.8	0,77,4223	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNMB3	NM_001163677.1,NM_014407.3,NM_171828.1,NM_171829.2,NM_171830.1	,,,,	0,83,6420	TT,TC,CC		0.8953,0.1362,0.6382	,,,,	122/174,124/280,122/278,102/258,120/276	178962370	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	27094	exon3			AAGACACGGGTAC	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.372G>A	3.37:g.178962370C>T		177.0	0.0	0		197.0	97.0	0.492386	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000314235.5	37	CCDS3226.1																																																																																			C|0.994;T|0.006	0.006	strong		0.498	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
BRAT1	221927	hgsc.bcm.edu	37	7	2578924	2578924	+	Silent	SNP	G	G	A	rs61746940	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2578924G>A	ENST00000340611.4	-	13	1915	c.1659C>T	c.(1657-1659)ctC>ctT	p.L553L	BRAT1_ENST00000473879.1_Intron	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	553					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GGTCCTGGAGGAGCTGCAGGG	0.647													G|||	2	0.000399361	0.0	0.0	5008	,	,		18093	0.0		0.001	False		,,,				2504	0.001				p.L553L		Atlas-SNP	.											.	BRAT1	57	.	0			c.C1659T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	31.0	31.0	31.0		1659	-5.8	0.8	7	dbSNP_129	31	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	BRAT1	NM_152743.3		0,30,6473	AA,AG,GG		0.3372,0.0227,0.2307		553/822	2578924	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	221927	exon13			CTGGAGGAGCTGC	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1659C>T	7.37:g.2578924G>A		122.0	0.0	0		162.0	70.0	0.432099	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
ACTG1	71	hgsc.bcm.edu	37	17	79479108	79479108	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479108G>A	ENST00000575842.1	-	2	610	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C	ACTG1_ENST00000331925.2_Missense_Mutation_p.R62C|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.R62C|ACTG1_ENST00000575087.1_Missense_Mutation_p.R62C|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	62					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			AGGATGCCACGCTTGCTCTGG	0.627																																					p.R62C		Atlas-SNP	.											.	ACTG1	55	.	0			c.C184T						PASS	.						70.0	68.0	68.0					17																	79479108		2203	4300	6503	SO:0001583	missense	71	exon3			TGCCACGCTTGCT		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.184C>T	17.37:g.79479108G>A	ENSP00000458162:p.Arg62Cys	69.0	0.0	0		37.0	9.0	0.243243	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.863019	0.32884	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.90955	-2.76	3.99	0.23	0.15372	Actin, conserved site (1);	0.000000	0.64402	U	0.000005	D	0.94341	0.8181	H	0.98786	4.33	0.58432	D	0.999991	P	0.50819	0.939	P	0.45406	0.479	D	0.94108	0.7368	10	0.87932	D	0	.	11.3287	0.49463	0.0:0.0:0.2975:0.7025	.	62	P63261	ACTG_HUMAN	C	62	ENSP00000331514:R62C	ENSP00000331514:R62C	R	-	1	0	ACTG1	77093703	1.000000	0.71417	0.758000	0.31321	0.728000	0.41692	3.215000	0.51169	0.236000	0.21180	0.563000	0.77884	CGT	.	.	none		0.627	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	
DHX32	55760	hgsc.bcm.edu	37	10	127541743	127541743	+	Intron	SNP	A	A	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127541743A>G	ENST00000284690.3	-	5	1583				DHX32_ENST00000284688.6_Intron|BCCIP_ENST00000368759.5_Silent_p.L300L|DHX32_ENST00000368721.1_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32							mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AGGCTGGACTAATTCAATCAA	0.433																																					p.L300L		Atlas-SNP	.											.	BCCIP	48	.	0			c.A900G						PASS	.						130.0	127.0	128.0					10																	127541743		2203	4300	6503	SO:0001627	intron_variant	56647	exon8			TGGACTAATTCAA		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"""DEAH-boxes"""	16717	protein-coding gene	gene with protein product		607960	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"""	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1093-532T>C	10.37:g.127541743A>G		79.0	0.0	0		61.0	28.0	0.459016	NM_016567	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	37	CCDS7652.1																																																																																			.	.	none		0.433	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180	
JAK1	3716	hgsc.bcm.edu	37	1	65313232	65313232	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:65313232G>A	ENST00000342505.4	-	13	2130	c.1882C>T	c.(1882-1884)Cac>Tac	p.H628Y	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	628	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.L624_R629>W(1)		breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATATCCCTGTGGCTGGGGTCT	0.488			Mis		ALL																																p.H628Y		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	1	Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1882T						PASS	.						213.0	222.0	219.0					1																	65313232		1890	4105	5995	SO:0001583	missense	3716	exon13			CCCTGTGGCTGGG	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1882C>T	1.37:g.65313232G>A	ENSP00000343204:p.His628Tyr	135.0	0.0	0		126.0	39.0	0.309524	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.662143	0.88251	.	.	ENSG00000162434	ENST00000342505	D	0.82344	-1.6	5.01	5.01	0.66863	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89897	0.6848	M	0.75884	2.315	0.58432	D	0.999998	D	0.76494	0.999	D	0.83275	0.996	D	0.89400	0.3695	9	0.54805	T	0.06	-8.2173	18.8858	0.92376	0.0:0.0:1.0:0.0	.	628	P23458	JAK1_HUMAN	Y	628	ENSP00000343204:H628Y	ENSP00000343204:H628Y	H	-	1	0	JAK1	65085820	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.295000	0.78780	2.775000	0.95449	0.655000	0.94253	CAC	.	.	none		0.488	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
SGK1	6446	hgsc.bcm.edu	37	6	134494280	134494280	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494280T>A	ENST00000237305.7	-	6	518	c.430A>T	c.(430-432)Atg>Ttg	p.M144L	SGK1_ENST00000528577.1_Missense_Mutation_p.M172L|SGK1_ENST00000413996.3_Missense_Mutation_p.M158L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.M134L|SGK1_ENST00000475719.2_Intron|SGK1_ENST00000367858.5_Missense_Mutation_p.M239L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		CGCTCCGACATAATATGCTTC	0.433																																					p.M239L		Atlas-SNP	.											.	SGK1	387	.	0			c.A715T						PASS	.						101.0	105.0	103.0					6																	134494280		2203	4300	6503	SO:0001583	missense	6446	exon8			CCGACATAATATG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.430A>T	6.37:g.134494280T>A	ENSP00000237305:p.Met144Leu	96.0	0.0	0		96.0	20.0	0.208333	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.130515	0.56828	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	6.04	6.04	0.98038	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	N	0.04297	-0.235	0.80722	D	1	D;D;P;D;D	0.56287	0.969;0.973;0.939;0.969;0.975	P;D;P;P;D	0.76575	0.891;0.988;0.721;0.891;0.934	T	0.53933	-0.8368	10	0.11182	T	0.66	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	172;158;134;239;144	O00141-5;O00141-3;O00141-4;O00141-2;O00141	.;.;.;.;SGK1_HUMAN	L	239;158;144;134;172	ENSP00000356832:M239L;ENSP00000396242:M158L;ENSP00000237305:M144L;ENSP00000356831:M134L;ENSP00000434450:M172L	ENSP00000237305:M144L	M	-	1	0	SGK1	134535973	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	6.264000	0.72527	2.317000	0.78254	0.460000	0.39030	ATG	.	.	none		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
DCANP1	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782396T>A	ENST00000503143.2	-	1	642	c.403A>T	c.(403-405)Agt>Tgt	p.S135C	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		135						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCTGAAACTACAAACCAGA	0.547													T|||	430	0.0858626	0.2867	0.0418	5008	,	,		19738	0.0		0.0179	False		,,,				2504	0.0041				p.S135C		Atlas-SNP	.											.	C5orf20	16	.	0			c.A403T						PASS	.	T	CYS/SER	1116,3290	402.4+/-332.3	149,818,1236	132.0	143.0	139.0		403	-1.8	0.0	5	dbSNP_130	139	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	112	150,935,5418	AA,AT,TT		1.3837,25.3291,9.4956	benign	135/245	134782396	1235,11771	2203	4300	6503	SO:0001583	missense	140947	exon1			TGAAACTACAAAC																												ENST00000503143.2:c.403A>T	5.37:g.134782396T>A	ENSP00000421871:p.Ser135Cys	76.0	0.0	0		79.0	31.0	0.392405	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	163	0.07463369963369963	132	0.2682926829268293	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	4.521	0.096694	0.08681	0.253291	0.013837	ENSG00000251380	ENST00000503143	T	0.39056	1.1	2.85	-1.79	0.07932	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	8	0.87932	D	0	.	4.0496	0.09790	0.3788:0.41:0.0:0.2112	.	135	Q8TF63	DCNP1_HUMAN	C	135	ENSP00000421871:S135C	ENSP00000421871:S135C	S	-	1	0	C5orf20	134810295	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.310000	0.19356	-0.278000	0.09180	-0.892000	0.02923	AGT	T|0.905;A|0.095	0.095	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
SYNE3	161176	hgsc.bcm.edu	37	14	95884294	95884294	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95884294G>A	ENST00000334258.5	-	17	2811	c.2797C>T	c.(2797-2799)Ctt>Ttt	p.L933F	SYNE3_ENST00000554873.1_Missense_Mutation_p.L690F|SYNE3_ENST00000557275.1_Missense_Mutation_p.L928F	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	933	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						agcagcagaagcagctgcagt	0.642																																					p.L933F		Atlas-SNP	.											.	SYNE3	130	.	0			c.C2797T						PASS	.						78.0	70.0	72.0					14																	95884294		2203	4300	6503	SO:0001583	missense	161176	exon17			GCAGAAGCAGCTG	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2797C>T	14.37:g.95884294G>A	ENSP00000334308:p.Leu933Phe	98.0	0.0	0		81.0	7.0	0.0864198	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461520	0.43736	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.35973	1.28;1.28;1.28	4.67	-0.221	0.13126	Klarsicht/ANC-1/syne-1 homology (2);	0.288824	0.18450	U	0.140875	T	0.33440	0.0863	L	0.51422	1.61	0.80722	D	1	B;B	0.30281	0.232;0.275	B;B	0.35607	0.13;0.206	T	0.22800	-1.0206	10	0.51188	T	0.08	-2.5151	11.5454	0.50690	0.3057:0.0:0.6943:0.0	.	928;933	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	F	933;690;928	ENSP00000334308:L933F;ENSP00000452154:L690F;ENSP00000450562:L928F	ENSP00000334308:L933F	L	-	1	0	C14orf49	94954047	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	2.722000	0.47269	0.043000	0.15746	0.289000	0.19496	CTT	.	.	none		0.642	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
ARAP3	64411	hgsc.bcm.edu	37	5	141052986	141052986	+	Missense_Mutation	SNP	C	C	T	rs150744263	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:141052986C>T	ENST00000239440.4	-	6	1019	c.954G>A	c.(952-954)atG>atA	p.M318I	ARAP3_ENST00000513878.1_5'Flank|ARAP3_ENST00000508305.1_Missense_Mutation_p.M240I	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	318	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TGCCAAAGTACATCAGACTCC	0.527													C|||	12	0.00239617	0.0015	0.0014	5008	,	,		17660	0.0		0.0089	False		,,,				2504	0.0				p.M318I		Atlas-SNP	.											.	ARAP3	139	.	0			c.G954A						PASS	.	C	ILE/MET	1,4405	2.1+/-5.4	0,1,2202	114.0	110.0	112.0		954	4.3	1.0	5	dbSNP_134	112	38,8562	26.3+/-74.7	0,38,4262	yes	missense	ARAP3	NM_022481.5	10	0,39,6464	TT,TC,CC		0.4419,0.0227,0.2999	possibly-damaging	318/1545	141052986	39,12967	2203	4300	6503	SO:0001583	missense	64411	exon6			AAAGTACATCAGA	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.954G>A	5.37:g.141052986C>T	ENSP00000239440:p.Met318Ile	259.0	1.0	0.003861		224.0	104.0	0.464286	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	16.27	3.074584	0.55646	2.27E-4	0.004419	ENSG00000120318	ENST00000522690;ENST00000508305;ENST00000239440;ENST00000504448	T;T;T	0.74737	-0.87;-0.87;-0.87	5.21	4.34	0.51931	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.144833	0.64402	D	0.000014	T	0.63757	0.2538	L	0.49640	1.575	0.80722	D	1	B;P	0.34934	0.42;0.476	B;B	0.38921	0.099;0.285	T	0.67252	-0.5717	10	0.44086	T	0.13	.	12.7252	0.57166	0.0:0.9185:0.0:0.0815	.	240;318	G5E9Y3;Q8WWN8	.;ARAP3_HUMAN	I	237;240;318;318	ENSP00000421826:M240I;ENSP00000239440:M318I;ENSP00000421148:M318I	ENSP00000239440:M318I	M	-	3	0	ARAP3	141033170	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.256000	0.51492	1.192000	0.43071	0.557000	0.71058	ATG	C|0.997;T|0.003	0.003	strong		0.527	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39191027	39191027	+	Missense_Mutation	SNP	G	G	A	rs140428118	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39191027G>A	ENST00000344363.5	-	1	80	c.47C>T	c.(46-48)aCc>aTc	p.T16I		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	16						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGTCCCACTGGTGGAGCAGCT	0.582													g|||	7	0.00139776	0.0	0.0043	5008	,	,		17184	0.0		0.004	False		,,,				2504	0.0				p.T16I		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.C47T						PASS	.	G	ILE/THR	2,3942		0,2,1970	52.0	59.0	56.0		47	3.2	0.8	17	dbSNP_134	56	33,8297		0,33,4132	no	missense	KRTAP1-3	NM_030966.1	89	0,35,6102	AA,AG,GG		0.3962,0.0507,0.2852	benign	16/168	39191027	35,12239	1972	4165	6137	SO:0001583	missense	81850	exon1			CCACTGGTGGAGC	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.47C>T	17.37:g.39191027G>A	ENSP00000344420:p.Thr16Ile	166.0	0.0	0		145.0	76.0	0.524138	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	8.061	0.768110	0.15983	5.07E-4	0.003962	ENSG00000221880	ENST00000344363	T	0.34275	1.37	4.17	3.21	0.36854	.	.	.	.	.	T	0.20861	0.0502	.	.	.	0.30763	N	0.743898	B	0.17852	0.024	B	0.27170	0.077	T	0.19257	-1.0311	8	0.40728	T	0.16	.	8.0851	0.30767	0.109:0.0:0.891:0.0	.	16	Q8IUG1	KRA13_HUMAN	I	16	ENSP00000344420:T16I	ENSP00000344420:T16I	T	-	2	0	KRTAP1-3	36444553	0.424000	0.25490	0.846000	0.33378	0.296000	0.27459	2.395000	0.44459	1.338000	0.45544	0.563000	0.77884	ACC	G|0.997;A|0.003	0.003	strong		0.582	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
ZFYVE20	64145	hgsc.bcm.edu	37	3	15126313	15126313	+	Missense_Mutation	SNP	C	C	T	rs578256587		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:15126313C>T	ENST00000253699.3	-	8	1140	c.527G>A	c.(526-528)cGc>cAc	p.R176H	ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000476527.2_Missense_Mutation_p.R176H|ZFYVE20_ENST00000435849.3_Missense_Mutation_p.R176H	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	176	Necessary for the correct targeting to endosomes.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						GCAGTGGTGGCGGCGGTTCCG	0.552													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15809	0.0		0.0	False		,,,				2504	0.0				p.R176H		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G527A						PASS	.						54.0	63.0	60.0					3																	15126313		2203	4300	6503	SO:0001583	missense	64145	exon8			TGGTGGCGGCGGT	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"""Zinc fingers, FYVE domain containing"""	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.527G>A	3.37:g.15126313C>T	ENSP00000253699:p.Arg176His	119.0	0.0	0		123.0	58.0	0.471545	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277929	0.95459	.	.	ENSG00000131381	ENST00000253699;ENST00000476527;ENST00000435849	T;T;T	0.77877	-1.13;-1.13;-1.13	5.33	4.46	0.54185	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.91050	0.7184	H	0.95611	3.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.93160	0.6557	10	0.87932	D	0	-14.4964	13.5262	0.61597	0.0:0.9252:0.0:0.0748	.	176;176	B4DWY8;Q9H1K0	.;RBNS5_HUMAN	H	176	ENSP00000253699:R176H;ENSP00000422551:R176H;ENSP00000391039:R176H	ENSP00000253699:R176H	R	-	2	0	ZFYVE20	15101317	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.813000	0.86123	1.248000	0.43934	0.484000	0.47621	CGC	.	.	none		0.552	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340	
UHRF2	115426	hgsc.bcm.edu	37	9	6413643	6413643	+	Splice_Site	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413643G>A	ENST00000276893.5	+	1	321	c.153G>A	c.(151-153)caG>caA	p.Q51Q	UHRF2_ENST00000381373.3_Splice_Site_p.Q51Q|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	51	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		GGGGCAAGCAGGTGAGGCGCG	0.726																																					p.Q51Q		Atlas-SNP	.											.	UHRF2	50	.	0			c.G153A						PASS	.						11.0	14.0	13.0					9																	6413643		2197	4297	6494	SO:0001630	splice_region_variant	115426	exon1			CAAGCAGGTGAGG	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.153+1G>A	9.37:g.6413643G>A		22.0	0.0	0		14.0	5.0	0.357143	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.726	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	Silent
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:132352230C>G	ENST00000310125.4	-	1	146	c.58G>C	c.(58-60)Gag>Cag	p.E20Q		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	20					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					GTCTGGTTCTCGTCCATTAAG	0.483													G|||	383	0.101457	0.2247	0.0389	3775	,	,		13274	0.002		0.0288	False		,,,				2504	0.0286				p.E20Q		Atlas-SNP	.											.	TFDP3	92	.	0			c.G58C						PASS	.	G	GLN/GLU	304,905		40,182,42,295,133	63.0	47.0	52.0		58	0.2	0.0	X	dbSNP_125	52	85,2306		3,62,17,735,774	yes	missense	TFDP3	NM_016521.2	29	43,244,59,1030,907	GG,GC,G,CC,C		3.555,25.1447,10.8056	benign	20/406	132352230	389,3211	692	1591	2283	SO:0001583	missense	51270	exon1			GGTTCTCGTCCAT	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.58G>C	X.37:g.132352230C>G	ENSP00000385461:p.Glu20Gln	66.0	0.0	0		134.0	52.0	0.38806	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	154	0.09282700421940929	74	0.17703349282296652	13	0.03651685393258427	2	0.0034965034965034965	14	0.01907356948228883	G	0.008	-1.897626	0.00517	0.251447	0.03555	ENSG00000183434	ENST00000310125	T	0.19806	2.12	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.00260	-1.75	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	7	0.02654	T	1	.	.	.	.	rs28455963	20	Q5H9I0	TFDP3_HUMAN	Q	20	ENSP00000385461:E20Q	ENSP00000385461:E20Q	E	-	1	0	TFDP3	132179896	0.988000	0.35896	0.016000	0.15963	0.016000	0.09150	0.556000	0.23438	-0.705000	0.05035	-0.699000	0.03677	GAG	C|0.877;G|0.123	0.123	strong		0.483	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
LDHAL6A	160287	hgsc.bcm.edu	37	11	18485611	18485611	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18485611T>C	ENST00000280706.2	+	2	1027	c.230T>C	c.(229-231)aTt>aCt	p.I77T	LDHAL6A_ENST00000396213.3_Missense_Mutation_p.I77T	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	77					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						ATGCCAAATATTGTCTCCAGC	0.343																																					p.I77T		Atlas-SNP	.											.	LDHAL6A	35	.	0			c.T230C						PASS	.						113.0	99.0	104.0					11																	18485611		2199	4293	6492	SO:0001583	missense	160287	exon2			CAAATATTGTCTC	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.230T>C	11.37:g.18485611T>C	ENSP00000280706:p.Ile77Thr	56.0	0.0	0		67.0	25.0	0.373134	NM_144972	D3DQY5	Missense_Mutation	SNP	ENST00000280706.2	37	CCDS7841.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.634138	0.47049	.	.	ENSG00000166800	ENST00000396213;ENST00000280706	D;D	0.90844	-2.74;-2.74	3.95	2.79	0.32731	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.64402	U	0.000010	D	0.94235	0.8149	M	0.81497	2.545	0.51767	D	0.99993	D	0.76494	0.999	D	0.76071	0.987	D	0.93050	0.6465	10	0.87932	D	0	.	9.3871	0.38349	0.0:0.0:0.1803:0.8196	.	77	Q6ZMR3	LDH6A_HUMAN	T	77	ENSP00000379516:I77T;ENSP00000280706:I77T	ENSP00000280706:I77T	I	+	2	0	LDHAL6A	18442187	1.000000	0.71417	0.327000	0.25402	0.745000	0.42441	4.294000	0.59043	0.400000	0.25396	0.533000	0.62120	ATT	.	.	none		0.343	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972	
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186121995A>T	ENST00000271588.4	+	96	15239	c.15010A>T	c.(15010-15012)Act>Tct	p.T5004S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGCTGAAGTCACTGTAAAGGT	0.438													A|||	9	0.00179712	0.0	0.0	5008	,	,		18499	0.0		0.008	False		,,,				2504	0.001				p.T5004S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A15010T						PASS	.	A	SER/THR	3,4403	4.2+/-10.8	0,3,2200	196.0	170.0	179.0		15010	0.8	0.1	1	dbSNP_133	179	28,8572	9.1+/-34.3	1,26,4273	yes	missense	HMCN1	NM_031935.2	58	1,29,6473	TT,TA,AA		0.3256,0.0681,0.2384	benign	5004/5636	186121995	31,12975	2203	4300	6503	SO:0001583	missense	83872	exon96			GAAGTCACTGTAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15010A>T	1.37:g.186121995A>T	ENSP00000271588:p.Thr5004Ser	158.0	0.0	0		169.0	72.0	0.426035	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	2.871	-0.233991	0.05983	6.81E-4	0.003256	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32988	1.43;1.43	5.9	0.836	0.18891	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32161	-0.9917	10	0.05833	T	0.94	.	6.2405	0.20787	0.6238:0.1195:0.2567:0.0	.	5004	Q96RW7	HMCN1_HUMAN	S	5004	ENSP00000271588:T5004S;ENSP00000356462:T5004S	ENSP00000271588:T5004S	T	+	1	0	HMCN1	184388618	0.001000	0.12720	0.065000	0.19835	0.779000	0.44077	0.806000	0.27126	-0.101000	0.12219	-0.263000	0.10527	ACT	A|0.996;T|0.004	0.004	strong		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HCFC1	3054	hgsc.bcm.edu	37	X	153223257	153223257	+	Silent	SNP	C	C	T	rs3027888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153223257C>T	ENST00000310441.7	-	12	3075	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	HCFC1_ENST00000369984.4_Silent_p.T703T|HCFC1_ENST00000354233.3_Silent_p.T634T|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	703	Interaction with SIN3A.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCACAGGACCCGTGGACGCCT	0.552													C|||	17	0.00450331	0.0	0.0	3775	,	,		16219	0.0		0.004	False		,,,				2504	0.0133				p.T703T		Atlas-SNP	.											.	HCFC1	284	.	0			c.G2109A						PASS	.	C		4,3432		0,4,0,1429,570	83.0	86.0	85.0		2109	-10.5	0.2	X	dbSNP_102	85	55,6449		0,39,16,2314,1782	no	coding-synonymous	HCFC1	NM_005334.2		0,43,16,3743,2352	TT,TC,T,CC,C		0.8456,0.1164,0.5936		703/2036	153223257	59,9881	2003	4151	6154	SO:0001819	synonymous_variant	3054	exon12			AGGACCCGTGGAC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2109G>A	X.37:g.153223257C>T		66.0	0.0	0		98.0	22.0	0.22449	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			C|0.998;T|0.002	0.002	strong		0.552	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
RORA	6095	hgsc.bcm.edu	37	15	61521304	61521304	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:61521304C>T	ENST00000335670.6	-	1	214	c.114G>A	c.(112-114)aaG>aaA	p.K38K		NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	38					angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						GCGGCTCGCTCTTGCGGGCGG	0.766																																					p.K38K		Atlas-SNP	.											.	RORA	114	.	0			c.G114A						PASS	.						5.0	5.0	5.0					15																	61521304		1830	3566	5396	SO:0001819	synonymous_variant	6095	exon1			CTCGCTCTTGCGG	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"""Nuclear hormone receptors"""	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.114G>A	15.37:g.61521304C>T		49.0	0.0	0		45.0	18.0	0.4	NM_134261	P35397|P35399|P45445|Q495X4|Q96H83	Silent	SNP	ENST00000335670.6	37	CCDS10177.1																																																																																			.	.	none		0.766	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		
TMEM155	132332	hgsc.bcm.edu	37	4	122682720	122682720	+	Missense_Mutation	SNP	C	C	T	rs138330999	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:122682720C>T	ENST00000337677.5	-	5	743	c.185G>A	c.(184-186)cGc>cAc	p.R62H	TMEM155_ENST00000394394.1_Missense_Mutation_p.R62H|TMEM155_ENST00000394396.1_Missense_Mutation_p.R62H	NM_152399.2	NP_689612.2	Q4W5P6	TM155_HUMAN	transmembrane protein 155	62						extracellular region (GO:0005576)				breast(1)|lung(5)	6						CCCCTGCAAGCGAACCAAAAA	0.378													C|||	18	0.00359425	0.0008	0.0072	5008	,	,		18627	0.0		0.0109	False		,,,				2504	0.001				p.R62H		Atlas-SNP	.											TMEM155,NS,carcinoma,0,1	TMEM155	17	1	0			c.G185A						PASS	.	C	HIS/ARG	9,4397	15.5+/-35.6	0,9,2194	61.0	63.0	62.0		185	-1.0	1.0	4	dbSNP_134	62	90,8510	49.8+/-109.6	2,86,4212	yes	missense	TMEM155	NM_152399.2	29	2,95,6406	TT,TC,CC		1.0465,0.2043,0.7612	possibly-damaging	62/131	122682720	99,12907	2203	4300	6503	SO:0001583	missense	132332	exon5			TGCAAGCGAACCA	AK055396	CCDS3721.1	4q27	2008-02-05			ENSG00000164112	ENSG00000164112			26418	protein-coding gene	gene with protein product							Standard	NM_152399		Approved	FLJ30834	uc003idx.1	Q4W5P6	OTTHUMG00000133035	ENST00000337677.5:c.185G>A	4.37:g.122682720C>T	ENSP00000336987:p.Arg62His	261.0	0.0	0		243.0	125.0	0.514403	NM_152399	D3DNW9|Q96NI2	Missense_Mutation	SNP	ENST00000337677.5	37	CCDS3721.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	11.78	1.741976	0.30865	0.002043	0.010465	ENSG00000164112	ENST00000394396;ENST00000337677;ENST00000394394;ENST00000514885	T;T;T;T	0.58797	0.46;0.46;0.46;0.31	5.23	-0.983	0.10263	.	0.327069	0.22175	N	0.063597	T	0.21427	0.0516	N	0.04508	-0.205	0.24235	N	0.995385	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	10	0.87932	D	0	-2.2114	6.5437	0.22394	0.0:0.0903:0.4863:0.4235	.	62	Q4W5P6	TM155_HUMAN	H	62	ENSP00000377919:R62H;ENSP00000336987:R62H;ENSP00000377917:R62H;ENSP00000422869:R62H	ENSP00000336987:R62H	R	-	2	0	TMEM155	122902170	0.974000	0.33945	0.992000	0.48379	0.996000	0.88848	0.148000	0.16224	0.114000	0.18032	-0.290000	0.09829	CGC	C|0.995;T|0.005	0.005	strong		0.378	TMEM155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256637.2	NM_152399	
ZNF577	84765	hgsc.bcm.edu	37	19	52375907	52375907	+	Silent	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52375907T>G	ENST00000301399.5	-	7	1701	c.1336A>C	c.(1336-1338)Aga>Cga	p.R446R	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Silent_p.R387R|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.R387R	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	446					regulation of transcription, DNA-templated (GO:0006355)|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)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GCTTGATTTCTTGGAAAAGGT	0.398																																					p.R446R		Atlas-SNP	.											ZNF577,colon,carcinoma,+1,1	ZNF577	63	1	0			c.A1336C						PASS	.						67.0	63.0	64.0					19																	52375907		2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			GATTTCTTGGAAA	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1336A>C	19.37:g.52375907T>G		83.0	0.0	0		76.0	17.0	0.223684	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.	.	none		0.398	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
HIST1H2AD	3013	hgsc.bcm.edu	37	6	26199193	26199193	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26199193C>T	ENST00000341023.1	-	1	278	c.279G>A	c.(277-279)gaG>gaA	p.E93E	HIST1H3D_ENST00000377831.5_5'UTR|HIST1H3D_ENST00000356476.2_5'Flank|HIST1H2BF_ENST00000359985.1_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	93						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E93D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				ACTTGTTTAGCTCCTCGTCGT	0.602																																					p.E93E		Atlas-SNP	.											HIST1H2AD,NS,lymphoid_neoplasm,0,1	HIST1H2AD	20	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G279A						PASS	.						128.0	121.0	123.0					6																	26199193		2203	4300	6503	SO:0001819	synonymous_variant	3013	exon1			GTTTAGCTCCTCG	Z80776	CCDS4591.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196866	ENSG00000196866		"""Histones / Replication-dependent"""	4729	protein-coding gene	gene with protein product		602792	"""H2A histone family, member G"", ""histone 1, H2ad"""	H2AFG		9119399, 12408966	Standard	NM_021065		Approved	H2A/g, H2A.3	uc003ngw.4	P20671	OTTHUMG00000014437	ENST00000341023.1:c.279G>A	6.37:g.26199193C>T		182.0	0.0	0		164.0	31.0	0.189024	NM_021065	A0PK91|P57754|Q6FGY6	Silent	SNP	ENST00000341023.1	37	CCDS4591.1																																																																																			.	.	none		0.602	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152250	151152250	+	Missense_Mutation	SNP	A	A	G	rs148178393	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:151152250A>G	ENST00000358517.2	+	15	2214	c.2003A>G	c.(2002-2004)gAc>gGc	p.D668G	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.D668G			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	668							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AGTTATGAGGACTTAAAACTA	0.478													A|||	26	0.00519169	0.0015	0.0144	5008	,	,		21879	0.0		0.0129	False		,,,				2504	0.001				p.D668G		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A2003G						PASS	.	A	GLY/ASP	13,4393	17.9+/-39.9	0,13,2190	45.0	45.0	45.0		2003	5.3	1.0	6	dbSNP_134	45	92,8508	51.1+/-111.2	0,92,4208	yes	missense	PLEKHG1	NM_001029884.1	94	0,105,6398	GG,GA,AA		1.0698,0.2951,0.8073	probably-damaging	668/1386	151152250	105,12901	2203	4300	6503	SO:0001583	missense	57480	exon16			ATGAGGACTTAAA	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2003A>G	6.37:g.151152250A>G	ENSP00000351318:p.Asp668Gly	55.0	0.0	0		71.0	35.0	0.492958	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	21	0.009615384615384616	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	12	0.0158311345646438	A	22.1	4.244378	0.79912	0.002951	0.010698	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.70516	-0.49;-0.49	5.31	5.31	0.75309	.	0.089123	0.85682	D	0.000000	T	0.78742	0.4331	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.984;0.976;0.976	T	0.82212	-0.0569	10	0.87932	D	0	.	15.3102	0.74026	1.0:0.0:0.0:0.0	.	475;668;668	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	G	668	ENSP00000356297:D668G;ENSP00000351318:D668G	ENSP00000351318:D668G	D	+	2	0	PLEKHG1	151193943	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	8.962000	0.93254	2.024000	0.59613	0.454000	0.30748	GAC	A|0.991;G|0.009	0.009	strong		0.478	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
GPR128	84873	hgsc.bcm.edu	37	3	100328750	100328750	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:100328750G>A	ENST00000273352.3	+	1	318	c.50G>A	c.(49-51)tGt>tAt	p.C17Y		NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	17					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GCTGTCGTGTGTGGACTACTG	0.493																																					p.C17Y	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.G50A						PASS	.						214.0	175.0	188.0					3																	100328750		2203	4300	6503	SO:0001583	missense	84873	exon1			TCGTGTGTGGACT	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.50G>A	3.37:g.100328750G>A	ENSP00000273352:p.Cys17Tyr	225.0	0.0	0		254.0	113.0	0.444882	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.730751	0.69074	.	.	ENSG00000144820	ENST00000273352	T	0.41400	1.0	5.69	1.54	0.23209	.	0.095269	0.46442	D	0.000299	T	0.36441	0.0967	M	0.65975	2.015	0.21020	N	0.999803	B	0.24721	0.11	B	0.24541	0.054	T	0.32052	-0.9921	10	0.51188	T	0.08	.	6.5832	0.22607	0.0853:0.0:0.4113:0.5034	.	17	Q96K78	GP128_HUMAN	Y	17	ENSP00000273352:C17Y	ENSP00000273352:C17Y	C	+	2	0	GPR128	101811440	0.916000	0.31088	0.744000	0.31058	0.497000	0.33675	0.814000	0.27239	0.678000	0.31325	0.563000	0.77884	TGT	.	.	none		0.493	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
PRKAA1	5562	hgsc.bcm.edu	37	5	40798278	40798278	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:40798278C>T	ENST00000397128.2	-	1	22	c.14G>A	c.(13-15)aGt>aAt	p.S5N	PRKAA1_ENST00000296800.4_5'Flank|PRKAA1_ENST00000354209.3_Missense_Mutation_p.S5N	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	5				S -> C (in Ref. 4; BAG35788). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TCTCCAGGAACTGAGTCTGCG	0.721																																					p.S5N		Atlas-SNP	.											.	PRKAA1	27	.	0			c.G14A						PASS	.						43.0	50.0	48.0					5																	40798278		2175	4295	6470	SO:0001583	missense	5562	exon1			CAGGAACTGAGTC		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.14G>A	5.37:g.40798278C>T	ENSP00000380317:p.Ser5Asn	83.0	0.0	0		117.0	22.0	0.188034	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	37	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922306	0.52653	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.73152	-0.66;-0.72	3.56	2.69	0.31865	.	0.555807	0.15939	U	0.237270	T	0.55816	0.1944	N	0.22421	0.69	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53394	-0.8445	10	0.62326	D	0.03	-0.1809	10.7188	0.46028	0.0:0.903:0.0:0.097	.	5;5	Q13131;Q13131-2	AAPK1_HUMAN;.	N	5	ENSP00000380317:S5N;ENSP00000346148:S5N	ENSP00000346148:S5N	S	-	2	0	AC008810.1	40834035	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	0.840000	0.27600	0.822000	0.34565	0.205000	0.17691	AGT	.	.	none		0.721	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
PLP2	5355	hgsc.bcm.edu	37	X	49029758	49029758	+	Silent	SNP	G	G	A	rs145837656		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49029758G>A	ENST00000376327.5	+	3	348	c.273G>A	c.(271-273)gcG>gcA	p.A91A	PLP2_ENST00000376322.3_Silent_p.A91A	NM_002668.2	NP_002659.1	Q04941	PLP2_HUMAN	proteolipid protein 2 (colonic epithelium-enriched)	91	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		A -> S (in dbSNP:rs1802969).		chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine binding (GO:0019956)|ion transmembrane transporter activity (GO:0015075)			endometrium(3)|large_intestine(1)|lung(6)|urinary_tract(3)	13						CCCTCATAGCGGCAATCCTCT	0.542																																					p.A91A		Atlas-SNP	.											.	PLP2	25	.	0			c.G273A						PASS	.	G		2,3833		0,2,0,1630,571	138.0	108.0	118.0		273	-10.7	0.0	X	dbSNP_134	118	3,6725		0,2,1,2426,1871	no	coding-synonymous	PLP2	NM_002668.2		0,4,1,4056,2442	AA,AG,A,GG,G		0.0446,0.0522,0.0473		91/153	49029758	5,10558	2203	4300	6503	SO:0001819	synonymous_variant	5355	exon3			CATAGCGGCAATC	L09604	CCDS14319.1	Xp11.23	2008-08-01			ENSG00000102007	ENSG00000102007			9087	protein-coding gene	gene with protein product	"""A4 differentiation-dependent protein"""	300112				8470895, 7622043	Standard	NM_002668		Approved	A4, A4-LSB, MGC126187	uc004dmx.3	Q04941	OTTHUMG00000021513	ENST00000376327.5:c.273G>A	X.37:g.49029758G>A		38.0	0.0	0		60.0	24.0	0.4	NM_002668	A6NDT7|Q32MM8	Silent	SNP	ENST00000376327.5	37	CCDS14319.1																																																																																			G|1.000;A|0.000	0.000	weak		0.542	PLP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056540.1	NM_002668	
LY6G5C	80741	hgsc.bcm.edu	37	6	31647044	31647044	+	Splice_Site	SNP	A	A	G	rs143778717	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31647044A>G	ENST00000383237.4	-	2	126	c.123T>C	c.(121-123)ggT>ggC	p.G41G	LY6G5C_ENST00000375858.3_Splice_Site_p.G38G|LY6G5C_ENST00000474395.1_5'UTR|LY6G5C_ENST00000375860.2_Splice_Site_p.G39G			Q5SRR4	LY65C_HUMAN	lymphocyte antigen 6 complex, locus G5C	41						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	7						GAACAAACTTACCTAGAACAC	0.557													A|||	2	0.000399361	0.0	0.0	5008	,	,		19799	0.0		0.0	False		,,,				2504	0.002				p.G41G		Atlas-SNP	.											.	LY6G5C	8	.	0			c.T123C						PASS	.	A		1,3019		0,1,1509	151.0	130.0	137.0		123	-1.2	0.1	6	dbSNP_134	137	3,5415		0,3,2706	yes	coding-synonymous-near-splice	LY6G5C	NM_025262.3		0,4,4215	GG,GA,AA		0.0554,0.0331,0.0474		41/151	31647044	4,8434	1510	2709	4219	SO:0001630	splice_region_variant	80741	exon2			AAACTTACCTAGA		CCDS34401.1, CCDS34401.2	6p21	2010-02-17	2002-07-29	2002-08-01	ENSG00000204428	ENSG00000204428			13932	protein-coding gene	gene with protein product		610434	"""chromosome 6 open reading frame 20"""	C6orf20		12079290	Standard	NM_025262		Approved	G5c, NG33	uc003nvu.2	Q5SRR4	OTTHUMG00000031228	ENST00000383237.4:c.122-1T>C	6.37:g.31647044A>G		80.0	0.0	0		69.0	18.0	0.26087	NM_025262	A6NCW4|B0UXB3|B0UXB4|B0UZ69|B0UZQ0|B1B0L9|O95871|Q5SQ59|Q8NDY0|Q8NDY1	Silent	SNP	ENST00000383237.4	37	CCDS34401.2	.	.	.	.	.	.	.	.	.	.	A	9.297	1.052217	0.19827	3.31E-4	5.54E-4	ENSG00000204428	ENST00000375863	.	.	.	2.93	-1.22	0.09494	.	.	.	.	.	T	0.24624	0.0597	.	.	.	0.44587	D	0.997556	.	.	.	.	.	.	T	0.25012	-1.0144	4	.	.	.	-3.476	2.375	0.04339	0.5268:0.0:0.2584:0.2149	.	.	.	.	A	116	.	.	V	-	2	0	LY6G5C	31755023	0.024000	0.19004	0.095000	0.20976	0.925000	0.55904	-0.071000	0.11505	-0.233000	0.09797	0.379000	0.24179	GTA	A|0.999;G|0.001	0.001	strong		0.557	LY6G5C-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076473.4		Silent
C9orf114	51490	hgsc.bcm.edu	37	9	131585086	131585086	+	Silent	SNP	G	G	C	rs35677895	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131585086G>C	ENST00000361256.5	-	12	1129	c.1089C>G	c.(1087-1089)gcC>gcG	p.A363A		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	363							poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CAGGCTGCAGGGCGGCCAGGG	0.662													G|||	25	0.00499201	0.0015	0.0058	5008	,	,		16485	0.0		0.0179	False		,,,				2504	0.001				p.A363A		Atlas-SNP	.											.	C9orf114	28	.	0			c.C1089G						PASS	.	G		13,4367		0,13,2177	33.0	33.0	33.0		1089	2.0	1.0	9	dbSNP_126	33	157,8421		0,157,4132	no	coding-synonymous	C9orf114	NM_016390.2		0,170,6309	CC,CG,GG		1.8303,0.2968,1.3119		363/377	131585086	170,12788	2190	4289	6479	SO:0001819	synonymous_variant	51490	exon12			CTGCAGGGCGGCC		CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.1089C>G	9.37:g.131585086G>C		97.0	0.0	0		119.0	63.0	0.529412	NM_016390	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	ENST00000361256.5	37	CCDS6913.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	11.45	1.642891	0.29246	0.002968	0.018303	ENSG00000198917	ENST00000372618	.	.	.	4.91	1.98	0.26296	.	0.844601	0.10689	N	0.645425	T	0.18173	0.0436	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24012	-1.0172	8	0.28530	T	0.3	-7.5275	1.3407	0.02154	0.2665:0.1449:0.44:0.1486	rs35677895	362	E7ESY7	.	R	362	.	ENSP00000361701:P362R	P	-	2	0	C9orf114	130624907	0.753000	0.28349	0.989000	0.46669	0.966000	0.64601	-0.116000	0.10724	0.644000	0.30656	0.455000	0.32223	CCC	G|0.990;C|0.010	0.010	strong		0.662	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390	
DHX33	56919	hgsc.bcm.edu	37	17	5364393	5364393	+	Missense_Mutation	SNP	A	A	G	rs141223137	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5364393A>G	ENST00000225296.3	-	4	915	c.715T>C	c.(715-717)Ttc>Ctc	p.F239L	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	239	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TACTGAGAGAACAGGTCCACA	0.507													A|||	6	0.00119808	0.0	0.0014	5008	,	,		16225	0.0		0.005	False		,,,				2504	0.0				p.F239L		Atlas-SNP	.											DHX33,NS,carcinoma,+2,3	DHX33	41	3	0			c.T715C						PASS	.	A	LEU/PHE,LEU/PHE	2,4404	2.1+/-5.4	0,2,2201	153.0	142.0	146.0		196,715	6.1	1.0	17	dbSNP_134	146	45,8555	29.6+/-80.5	0,45,4255	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	22,22	0,47,6456	GG,GA,AA		0.5233,0.0454,0.3614	probably-damaging,probably-damaging	66/535,239/708	5364393	47,12959	2203	4300	6503	SO:0001583	missense	56919	exon4			GAGAGAACAGGTC	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.715T>C	17.37:g.5364393A>G	ENSP00000225296:p.Phe239Leu	61.0	0.0	0		70.0	28.0	0.4	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	36	5.656465	0.96724	4.54E-4	0.005233	ENSG00000005100	ENST00000225296	T	0.23348	1.91	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	M	0.63428	1.95	0.80722	D	1	D	0.63880	0.993	P	0.62014	0.897	T	0.36311	-0.9753	10	0.87932	D	0	.	15.81	0.78552	1.0:0.0:0.0:0.0	.	239	Q9H6R0	DHX33_HUMAN	L	239	ENSP00000225296:F239L	ENSP00000225296:F239L	F	-	1	0	DHX33	5305117	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	9.271000	0.95698	2.326000	0.78906	0.533000	0.62120	TTC	A|0.996;G|0.004	0.004	strong		0.507	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84610059	84610059	+	Silent	SNP	T	T	C	rs200816660	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84610059T>C	ENST00000344803.2	+	4	4721	c.4674T>C	c.(4672-4674)acT>acC	p.T1558T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1558					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTTTCCTAACTGGACAGAAAA	0.473													T|||	7	0.00139776	0.0	0.0	5008	,	,		18402	0.0		0.007	False		,,,				2504	0.0				p.T1558T		Atlas-SNP	.											.	.	.	.	0			c.T4674C						PASS	.	T		2,3956		0,2,1977	14.0	14.0	14.0		4674	-1.9	0.0	9		14	26,8304		0,26,4139	no	coding-synonymous	FAM75D1	NM_001001670.2		0,28,6116	CC,CT,TT		0.3121,0.0505,0.2279		1558/1577	84610059	28,12260	1979	4165	6144	SO:0001819	synonymous_variant	389763	exon4			CCTAACTGGACAG		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4674T>C	9.37:g.84610059T>C		29.0	0.0	0		18.0	11.0	0.611111	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
DUSP8	1850	hgsc.bcm.edu	37	11	1580172	1580172	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1580172T>A	ENST00000397374.3	-	4	611	c.484A>T	c.(484-486)Acc>Tcc	p.T162S	DUSP8_ENST00000331588.4_Missense_Mutation_p.T162S|DUSP8_ENST00000528778.1_5'UTR	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	162	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|lung(2)|prostate(1)|urinary_tract(1)	5		all_epithelial(84;0.000134)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000621)|Lung(200;0.0687)|LUSC - Lung squamous cell carcinoma(625;0.0825)		AGGATGCGGGTCAGGCCCACG	0.652																																					p.T162S		Atlas-SNP	.											.	DUSP8	22	.	0			c.A484T						PASS	.						93.0	78.0	83.0					11																	1580172		2202	4299	6501	SO:0001583	missense	1850	exon4			TGCGGGTCAGGCC		CCDS7724.1	11p15.5	2011-06-09			ENSG00000184545	ENSG00000184545		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3074	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""H1 phosphatase, vaccinia virus homolog"""	602038	"""chromosome 11 open reading frame 81"""	C11orf81		7561881, 9192849	Standard	NM_004420		Approved	HVH-5, HB5, FLJ42958	uc001lts.2	Q13202	OTTHUMG00000133348	ENST00000397374.3:c.484A>T	11.37:g.1580172T>A	ENSP00000380530:p.Thr162Ser	119.0	0.0	0		121.0	34.0	0.280992	NM_004420	Q86SS8	Missense_Mutation	SNP	ENST00000397374.3	37	CCDS7724.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.276345	0.59649	.	.	ENSG00000184545	ENST00000397374;ENST00000331588	T;T	0.56611	0.45;0.45	4.18	4.18	0.49190	Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.53938	U	0.000049	T	0.38692	0.1050	N	0.12746	0.255	0.58432	D	0.999999	B	0.31077	0.307	B	0.36092	0.217	T	0.46247	-0.9205	10	0.72032	D	0.01	.	13.4127	0.60952	0.0:0.0:0.0:1.0	.	162	Q13202	DUS8_HUMAN	S	162	ENSP00000380530:T162S;ENSP00000329539:T162S	ENSP00000329539:T162S	T	-	1	0	DUSP8	1536748	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.637000	0.83313	1.762000	0.52044	0.448000	0.29417	ACC	.	.	none		0.652	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420	
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55238874T>A	ENST00000275493.2	+	16	2064	c.1887T>A	c.(1885-1887)acT>acA	p.T629T	EGFR_ENST00000454757.2_Silent_p.T576T|EGFR_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	629					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	ACAGATGCACTGGGCCAGGTC	0.398		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			T|||	1955	0.390375	0.2678	0.3977	5008	,	,		21298	0.5347		0.3559	False		,,,				2504	0.4376				p.T629T		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.T1887A						PASS	.	T		1213,3193	422.3+/-339.7	168,877,1158	135.0	120.0	125.0		1887	-5.9	0.0	7	dbSNP_123	125	2981,5619	461.9+/-365.5	537,1907,1856	no	coding-synonymous	EGFR	NM_005228.3		705,2784,3014	AA,AT,TT		34.6628,27.5306,32.2467		629/1211	55238874	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATGCACTGGGCCA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1887T>A	7.37:g.55238874T>A		59.0	0.0	0		40.0	14.0	0.35	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			T|0.645;A|0.355	0.355	strong		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
CYP26A1	1592	hgsc.bcm.edu	37	10	94835624	94835624	+	Silent	SNP	C	C	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:94835624C>T	ENST00000224356.4	+	5	951	c.906C>T	c.(904-906)caC>caT	p.H302H	CYP26A1_ENST00000371531.1_Silent_p.H233H|CYP26A1_ENST00000394139.1_Silent_p.H233H	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	302					anterior/posterior pattern specification (GO:0009952)|cellular response to retinoic acid (GO:0071300)|central nervous system development (GO:0007417)|metabolic process (GO:0008152)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Colorectal(252;0.122)			Acitretin(DB00459)|Ketoconazole(DB01026)|Vitamin A(DB00162)	TTGGAGGACACGAAACCACGG	0.498																																					p.H302H		Atlas-SNP	.											.	CYP26A1	59	.	0			c.C906T						PASS	.						80.0	76.0	78.0					10																	94835624		2203	4300	6503	SO:0001819	synonymous_variant	1592	exon5			AGGACACGAAACC	AF005418	CCDS7426.1, CCDS7427.1	10q23-q24	2003-10-06	2003-01-14		ENSG00000095596	ENSG00000095596		"""Cytochrome P450s"""	2603	protein-coding gene	gene with protein product		602239	"""cytochrome P450, subfamily XXVIA, polypeptide 1"""			9228017, 9521883	Standard	NM_000783		Approved	P450RAI, CP26, CYP26, P450RAI1	uc001kil.2	O43174	OTTHUMG00000018765	ENST00000224356.4:c.906C>T	10.37:g.94835624C>T		75.0	0.0	0		94.0	4.0	0.0425532	NM_000783	B3KNI4|Q5VXH9|Q5VXI0	Silent	SNP	ENST00000224356.4	37	CCDS7426.1																																																																																			.	.	none		0.498	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3		
TNK2	10188	hgsc.bcm.edu	37	3	195594931	195594931	+	Silent	SNP	C	C	T	rs200272067	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195594931C>T	ENST00000333602.6	-	12	2810	c.2193G>A	c.(2191-2193)ccG>ccA	p.P731P	TNK2_ENST00000381916.2_Silent_p.P809P|TNK2_ENST00000428187.1_Silent_p.P763P|TNK2_ENST00000392400.1_Silent_p.P731P	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	731	Pro-rich.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CGTCACCCCCCGGGCTGGGAG	0.726													c|||	34	0.00678914	0.0151	0.0014	5008	,	,		12349	0.0		0.003	False		,,,				2504	0.0102				p.P809P		Atlas-SNP	.											.	TNK2	246	.	0			c.G2427A						PASS	.		,	18,4172		0,18,2077	6.0	9.0	8.0		2427,2193	-8.3	0.0	3		8	16,8346		0,16,4165	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	0,34,6242	TT,TC,CC		0.1913,0.4296,0.2709	,	809/1087,731/1039	195594931	34,12518	2095	4181	6276	SO:0001819	synonymous_variant	10188	exon13			ACCCCCCGGGCTG	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2193G>A	3.37:g.195594931C>T		50.0	0.0	0		45.0	21.0	0.466667	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																			C|0.997;T|0.003	0.003	strong		0.726	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704490	19704490	+	Splice_Site	SNP	G	G	A	rs146718638		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:19704490G>A	ENST00000284885.3	-	14	1598	c.1565C>T	c.(1564-1566)aCg>aTg	p.T522M		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	522						brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCCACAGTCCGCTGAAAAGGA	0.383													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17327	0.0		0.0	False		,,,				2504	0.0				p.T522M		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C1565T						PASS	.	G	MET/THR	0,4406		0,0,2203	102.0	101.0	102.0		1565	5.4	1.0	21	dbSNP_134	102	6,8594	5.0+/-18.6	0,6,4294	yes	missense-near-splice	TMPRSS15	NM_002772.2	81	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	522/1020	19704490	6,13000	2203	4300	6503	SO:0001630	splice_region_variant	5651	exon14			CAGTCCGCTGAAA		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1565-1C>T	21.37:g.19704490G>A		62.0	0.0	0		84.0	36.0	0.428571	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.095356	0.76870	0.0	6.98E-4	ENSG00000154646	ENST00000284885	D	0.87179	-2.22	5.43	5.43	0.79202	CUB (1);	0.124734	0.53938	D	0.000053	D	0.91758	0.7393	L	0.60455	1.87	0.42859	D	0.994106	D	0.89917	1.0	D	0.67382	0.951	D	0.90913	0.4777	9	.	.	.	.	18.1722	0.89749	0.0:0.0:1.0:0.0	.	522	P98073	ENTK_HUMAN	M	522	ENSP00000284885:T522M	.	T	-	2	0	TMPRSS15	18626361	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.749000	0.62155	2.705000	0.92388	0.650000	0.86243	ACG	G|1.000;A|0.000	0.000	weak		0.383	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	Missense_Mutation
CHMP1A	5119	hgsc.bcm.edu	37	16	89715813	89715813	+	Silent	SNP	C	C	T	rs201479143	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89715813C>T	ENST00000397901.3	-	4	454	c.198G>A	c.(196-198)gcG>gcA	p.A66A	CHMP1A_ENST00000253475.5_Missense_Mutation_p.V60I|CHMP1A_ENST00000535997.2_Silent_p.A2A|CHMP1A_ENST00000550102.1_Silent_p.A66A|CHMP1A_ENST00000547614.1_5'UTR	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	66					cytokinesis (GO:0000910)|gene silencing (GO:0016458)|mitotic chromosome condensation (GO:0007076)|negative regulation of transcription by glucose (GO:0045014)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|proteolysis (GO:0006508)|transcription, DNA-templated (GO:0006351)|vesicle-mediated transport (GO:0016192)	condensed nuclear chromosome (GO:0000794)|early endosome (GO:0005769)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|nuclear matrix (GO:0016363)	metallopeptidase activity (GO:0008237)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|ovary(1)	3		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.048)		CTACGCGGGACGCCATCCGAA	0.592													C|||	2	0.000399361	0.0	0.0	5008	,	,		14103	0.001		0.001	False		,,,				2504	0.0				p.V60I		Atlas-SNP	.											.	CHMP1A	15	.	0			c.G178A						PASS	.	C	ILE/VAL,	1,4321		0,1,2160	90.0	104.0	100.0		178,198	-6.3	1.0	16		100	14,8498		0,14,4242	yes	missense,coding-synonymous	CHMP1A	NM_001083314.1,NM_002768.2	29,	0,15,6402	TT,TC,CC		0.1645,0.0231,0.1169	,	60/241,66/197	89715813	15,12819	2161	4256	6417	SO:0001819	synonymous_variant	5119	exon3			GCGGGACGCCATC	U58048	CCDS45552.1	16q24.3	2011-09-21	2011-09-21	2007-03-20	ENSG00000131165	ENSG00000131165		"""Charged multivesicular body proteins"""	8740	protein-coding gene	gene with protein product		164010	"""procollagen (type III) N-endopeptidase"", ""chromatin modifying protein 1A"""	PRSM1, PCOLN3		11559748, 11559747	Standard	NM_002768		Approved	KIAA0047, CHMP1, Vps46A	uc002fnu.4	Q9HD42	OTTHUMG00000169521	ENST00000397901.3:c.198G>A	16.37:g.89715813C>T		92.0	0.0	0		80.0	44.0	0.55	NM_001083314	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.40	1.926176	0.34002	2.31E-4	0.001645	ENSG00000131165	ENST00000253475	.	.	.	5.38	-6.34	0.01982	.	0.936287	0.08656	N	0.913147	T	0.18215	0.0437	.	.	.	0.19945	N	0.999941	B	0.23891	0.093	B	0.17098	0.017	T	0.32107	-0.9919	8	0.87932	D	0	0.3661	0.8968	0.01265	0.1559:0.2634:0.2432:0.3375	.	60	A6NG32	.	I	60	.	ENSP00000253475:V60I	V	-	1	0	CHMP1A	88243314	0.000000	0.05858	0.964000	0.40570	0.730000	0.41778	-4.815000	0.00182	-0.773000	0.04596	-0.258000	0.10820	GTC	C|0.999;T|0.001	0.001	strong		0.592	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768	
SCAF8	22828	hgsc.bcm.edu	37	6	155114112	155114112	+	Splice_Site	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155114112T>A	ENST00000367178.3	+	5	1051		c.e5+2		SCAF8_ENST00000367186.4_Splice_Site|SCAF8_ENST00000417268.1_Splice_Site	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						ATACTCCAGGTATGTTGCTTT	0.398																																					.		Atlas-SNP	.											.	SCAF8	122	.	0			c.475+2T>A						PASS	.						60.0	59.0	60.0					6																	155114112		2203	4300	6503	SO:0001630	splice_region_variant	22828	exon5			TCCAGGTATGTTG	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.475+2T>A	6.37:g.155114112T>A		84.0	0.0	0		61.0	26.0	0.42623	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Splice_Site	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126604	0.56721	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	.	.	.	4.47	3.25	0.37280	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2621	0.43434	0.1485:0.0:0.0:0.8515	.	.	.	.	.	-1	.	.	.	+	.	.	SCAF8	155155804	1.000000	0.71417	0.994000	0.49952	0.766000	0.43426	6.932000	0.75869	0.629000	0.30376	0.379000	0.24179	.	.	.	none		0.398	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	Intron
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383217	39383217	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39383217G>A	ENST00000377721.3	+	1	318	c.311G>A	c.(310-312)aGc>aAc	p.S104N	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.S88N	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	104	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TGTGGGTCCAGCTGTGGCCAG	0.622																																					p.S104N		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.G311A						PASS	.						54.0	57.0	56.0					17																	39383217		2202	4293	6495	SO:0001583	missense	83899	exon1			GGTCCAGCTGTGG	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.311G>A	17.37:g.39383217G>A	ENSP00000366950:p.Ser104Asn	148.0	0.0	0		132.0	42.0	0.318182	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551968	0.27739	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01838	4.61;4.61	2.56	2.56	0.30785	.	.	.	.	.	T	0.02970	0.0088	M	0.67700	2.07	0.19300	N	0.999971	P	0.48016	0.904	B	0.36922	0.236	T	0.43605	-0.9381	9	0.48119	T	0.1	.	6.8345	0.23929	0.0:0.0:0.7231:0.2769	.	104	Q9BYQ4	KRA92_HUMAN	N	104;88	ENSP00000366950:S104N;ENSP00000398325:S88N	ENSP00000366950:S104N	S	+	2	0	KRTAP9-2	36636743	0.898000	0.30612	0.791000	0.31998	0.013000	0.08279	0.446000	0.21694	1.736000	0.51660	0.494000	0.49563	AGC	.	.	none		0.622	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
DNMT3L	29947	hgsc.bcm.edu	37	21	45670790	45670790	+	Missense_Mutation	SNP	C	C	T	rs113593938	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45670790C>T	ENST00000418993.1	-	10	1295	c.812G>A	c.(811-813)cGg>cAg	p.R271Q	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R271Q|AP001059.5_ENST00000442785.1_RNA	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	271					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		TGGCTTGGGCCGTGCGTACTG	0.657													C|||	10	0.00199681	0.0	0.0043	5008	,	,		10001	0.0		0.007	False		,,,				2504	0.0				p.R271Q		Atlas-SNP	.											.	DNMT3L	33	.	0			c.G812A						PASS	.	C	GLN/ARG,GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	45.0	39.0	41.0		812,812	1.6	0.0	21	dbSNP_132	41	43,8557	28.5+/-78.6	1,41,4258	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	43,43	1,45,6457	TT,TC,CC		0.5,0.0908,0.3614	possibly-damaging,possibly-damaging	271/388,271/387	45670790	47,12959	2203	4300	6503	SO:0001583	missense	29947	exon10			TTGGGCCGTGCGT	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"""cytosine-5-methyltransferase 3-like protein"", ""human cytosine-5-methyltransferase 3-like protein"""	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.812G>A	21.37:g.45670790C>T	ENSP00000412862:p.Arg271Gln	110.0	0.0	0		159.0	88.0	0.553459	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	C|C	8.432|8.432	0.848933|0.848933	0.17034|0.17034	9.08E-4|9.08E-4	0.005|0.005	ENSG00000142182|ENSG00000142182	ENST00000436357|ENST00000270172;ENST00000418993;ENST00000431166	.|T;T;T	.|0.32753	.|1.44;1.44;1.44	3.53|3.53	1.61|1.61	0.23674|0.23674	.|.	.|0.311404	.|0.28815	.|N	.|0.014056	T|T	0.19604|0.19604	0.0471|0.0471	M|M	0.75777|0.75777	2.31|2.31	0.24644|0.24644	N|N	0.99355|0.99355	.|B;B	.|0.29115	.|0.233;0.233	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.19582|0.19582	-1.0301|-1.0301	5|10	.|0.59425	.|D	.|0.04	-5.898|-5.898	5.0926|5.0926	0.14715|0.14715	0.2011:0.6813:0.0:0.1176|0.2011:0.6813:0.0:0.1176	.|.	.|271;271	.|Q9UJW3-2;Q9UJW3	.|.;DNM3L_HUMAN	S|Q	66|271;271;256	.|ENSP00000270172:R271Q;ENSP00000412862:R271Q;ENSP00000400242:R256Q	.|ENSP00000270172:R271Q	G|R	-|-	1|2	0|0	DNMT3L|DNMT3L	44495218|44495218	0.001000|0.001000	0.12720|0.12720	0.014000|0.014000	0.15608|0.15608	0.045000|0.045000	0.14185|0.14185	-0.211000|-0.211000	0.09332|0.09332	0.229000|0.229000	0.21039|0.21039	0.555000|0.555000	0.69702|0.69702	GGC|CGG	C|0.996;T|0.004	0.004	strong		0.657	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369	
MAML2	84441	hgsc.bcm.edu	37	11	95713077	95713077	+	Missense_Mutation	SNP	C	C	T	rs34520053	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:95713077C>T	ENST00000524717.1	-	5	3790	c.2506G>A	c.(2506-2508)Gtt>Att	p.V836I		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	836				V -> I (in Ref. 6; CAH10491). {ECO:0000305}.	gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TGTGTTGAAACTGGGTTTGCC	0.418			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid								C|||	31	0.0061901	0.0	0.0014	5008	,	,		20202	0.001		0.0229	False		,,,				2504	0.0061				p.V836I		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G2506A						PASS	.	C	ILE/VAL	23,3755		0,23,1866	142.0	134.0	136.0		2506	5.3	1.0	11	dbSNP_126	136	202,8038		2,198,3920	yes	missense	MAML2	NM_032427.1	29	2,221,5786	TT,TC,CC		2.4515,0.6088,1.8722	possibly-damaging	836/1157	95713077	225,11793	1889	4120	6009	SO:0001583	missense	84441	exon5			TTGAAACTGGGTT	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.2506G>A	11.37:g.95713077C>T	ENSP00000434552:p.Val836Ile	149.0	0.0	0		191.0	37.0	0.193717	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	C	6.771	0.511215	0.12883	0.006088	0.024515	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.44083	0.93;0.93	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000015	T	0.12732	0.0309	N	0.14661	0.345	0.35651	D	0.811778	B	0.27351	0.176	B	0.26517	0.07	T	0.21314	-1.0249	10	0.21540	T	0.41	-15.338	10.589	0.45298	0.0:0.8812:0.0:0.1188	rs34520053	836	Q8IZL2	MAML2_HUMAN	I	836	ENSP00000434552:V836I;ENSP00000412394:V836I	ENSP00000412394:V836I	V	-	1	0	MAML2	95352725	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	3.735000	0.55044	2.655000	0.90218	0.650000	0.86243	GTT	C|0.986;T|0.014	0.014	strong		0.418	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
SERPINA10	51156	hgsc.bcm.edu	37	14	94750408	94750408	+	Missense_Mutation	SNP	A	A	C	rs117152910	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94750408A>C	ENST00000393096.1	-	5	1694	c.1229T>G	c.(1228-1230)aTg>aGg	p.M410R	SERPINA10_ENST00000554723.1_Missense_Mutation_p.M450R|SERPINA10_ENST00000261994.4_Missense_Mutation_p.M410R|SERPINA10_ENST00000554173.1_Missense_Mutation_p.M410R	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	410					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GACAGGAGGCATGGAATAAGC	0.443													A|||	70	0.0139776	0.0	0.0	5008	,	,		18909	0.0188		0.0	False		,,,				2504	0.0521				p.M410R		Atlas-SNP	.											SERPINA10,caecum,carcinoma,+1,1	SERPINA10	83	1	0			c.T1229G						PASS	.	A	ARG/MET,ARG/MET	1,4405	2.1+/-5.4	0,1,2202	100.0	93.0	95.0		1229,1229	3.4	0.7	14	dbSNP_132	95	0,8600		0,0,4300	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	91,91	0,1,6502	CC,CA,AA		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	410/445,410/445	94750408	1,13005	2203	4300	6503	SO:0001583	missense	51156	exon5			GGAGGCATGGAAT	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.1229T>G	14.37:g.94750408A>C	ENSP00000376809:p.Met410Arg	60.0	0.0	0		86.0	42.0	0.488372	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	11	0.005036630036630037	0	0.0	0	0.0	11	0.019230769230769232	0	0.0	A	6.486	0.457830	0.12342	2.27E-4	0.0	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77	5.7	3.37	0.38596	Serpin domain (3);	0.158112	0.44285	D	0.000475	T	0.68632	0.3022	L	0.41710	1.295	0.32273	N	0.568655	P	0.51537	0.946	P	0.51135	0.66	T	0.76753	-0.2843	10	0.38643	T	0.18	.	9.8433	0.41013	0.8623:0.0:0.1377:0.0	.	410	Q9UK55	ZPI_HUMAN	R	450;410;410;410	ENSP00000450896:M450R;ENSP00000376809:M410R;ENSP00000261994:M410R;ENSP00000450971:M410R	ENSP00000261994:M410R	M	-	2	0	SERPINA10	93820161	0.979000	0.34478	0.707000	0.30419	0.005000	0.04900	1.686000	0.37669	0.448000	0.26722	-0.263000	0.10527	ATG	A|0.993;C|0.007	0.007	strong		0.443	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
GPR20	2843	hgsc.bcm.edu	37	8	142367087	142367087	+	Missense_Mutation	SNP	C	C	T	rs34591516	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:142367087C>T	ENST00000377741.3	-	2	1027	c.937G>A	c.(937-939)Ggc>Agc	p.G313S	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	313			G -> S (in dbSNP:rs34591516).		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			CCGTGCTGGCCGAAGAGGCCT	0.652													C|||	243	0.0485224	0.1051	0.062	5008	,	,		19947	0.0		0.0517	False		,,,				2504	0.0092				p.G313S		Atlas-SNP	.											.	GPR20	43	.	0			c.G937A						PASS	.	C	SER/GLY	422,3984	204.1+/-226.4	18,386,1799	73.0	63.0	67.0		937	1.2	0.1	8	dbSNP_126	67	491,8109	142.3+/-198.5	15,461,3824	yes	missense	GPR20	NM_005293.2	56	33,847,5623	TT,TC,CC		5.7093,9.5778,7.0198	benign	313/359	142367087	913,12093	2203	4300	6503	SO:0001583	missense	2843	exon2			GCTGGCCGAAGAG	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.937G>A	8.37:g.142367087C>T	ENSP00000366970:p.Gly313Ser	103.0	0.0	0		80.0	36.0	0.45	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	119	0.05448717948717949	60	0.12195121951219512	27	0.07458563535911603	0	0.0	32	0.04221635883905013	C	1.474	-0.559060	0.03967	0.095778	0.057093	ENSG00000204882	ENST00000377741	T	0.37235	1.21	5.21	1.16	0.20824	.	1.376680	0.05461	U	0.551317	T	0.00241	0.0007	N	0.14661	0.345	0.09310	N	0.999998	B	0.29671	0.254	B	0.16289	0.015	T	0.08597	-1.0714	10	0.09084	T	0.74	-5.6003	3.7924	0.08726	0.0829:0.3719:0.3049:0.2403	rs34591516	313	Q99678	GPR20_HUMAN	S	313	ENSP00000366970:G313S	ENSP00000366970:G313S	G	-	1	0	GPR20	142436269	0.202000	0.23423	0.092000	0.20876	0.040000	0.13550	0.335000	0.19806	-0.079000	0.12707	-0.311000	0.09066	GGC	C|0.934;T|0.066	0.066	strong		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
DMRT3	58524	hgsc.bcm.edu	37	9	990235	990235	+	Missense_Mutation	SNP	C	C	T	rs61737966	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:990235C>T	ENST00000190165.2	+	2	687	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	217					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CCCCGAGAGCCGCCCTGACAG	0.597													C|||	10	0.00199681	0.0	0.0101	5008	,	,		16117	0.0		0.003	False		,,,				2504	0.0				p.R217C		Atlas-SNP	.											.	DMRT3	83	.	0			c.C649T						PASS	.	C	CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	50.0	59.0	56.0		649	1.5	0.8	9	dbSNP_129	56	56,8544	35.9+/-90.5	0,56,4244	yes	missense	DMRT3	NM_021240.2	180	0,61,6442	TT,TC,CC		0.6512,0.1135,0.469	benign	217/473	990235	61,12945	2203	4300	6503	SO:0001583	missense	58524	exon2			GAGAGCCGCCCTG	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.649C>T	9.37:g.990235C>T	ENSP00000190165:p.Arg217Cys	35.0	0.0	0		29.0	16.0	0.551724	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	5.112	0.206206	0.09704	0.001135	0.006512	ENSG00000064218	ENST00000190165;ENST00000417254	T;T	0.32515	1.45;1.45	4.8	1.49	0.22878	.	0.471170	0.18808	N	0.130585	T	0.19046	0.0457	L	0.54323	1.7	0.33463	D	0.58522	B	0.09022	0.002	B	0.04013	0.001	T	0.25398	-1.0133	10	0.52906	T	0.07	-11.9879	7.7357	0.28812	0.3549:0.5579:0.0:0.0872	rs61737966	217	Q9NQL9	DMRT3_HUMAN	C	217;80	ENSP00000190165:R217C;ENSP00000387472:R80C	ENSP00000190165:R217C	R	+	1	0	DMRT3	980235	1.000000	0.71417	0.788000	0.31933	0.031000	0.12232	2.448000	0.44926	0.991000	0.38814	0.455000	0.32223	CGC	C|0.995;T|0.005	0.005	strong		0.597	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
NBEAL2	23218	hgsc.bcm.edu	37	3	47046485	47046485	+	Silent	SNP	C	C	T	rs141569354	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:47046485C>T	ENST00000450053.3	+	39	6497	c.6318C>T	c.(6316-6318)taC>taT	p.Y2106Y	NBEAL2_ENST00000383740.2_Silent_p.Y385Y|NBEAL2_ENST00000292309.5_Silent_p.Y1922Y	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2106	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGCAGGACTACGTGTCCCCAA	0.662													C|||	15	0.00299521	0.0	0.0043	5008	,	,		17699	0.0		0.0119	False		,,,				2504	0.0				p.Y2106Y		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C6318T						PASS	.	C		9,4051		0,9,2021	41.0	47.0	45.0		6318	-1.1	1.0	3	dbSNP_134	45	100,8250		0,100,4075	no	coding-synonymous	NBEAL2	NM_015175.1		0,109,6096	TT,TC,CC		1.1976,0.2217,0.8783		2106/2755	47046485	109,12301	2030	4175	6205	SO:0001819	synonymous_variant	23218	exon39			GGACTACGTGTCC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6318C>T	3.37:g.47046485C>T		84.0	0.0	0		86.0	39.0	0.453488	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	11|11	0.005036630036630037|0.005036630036630037	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	7.555|7.555	0.663419|0.663419	0.14710|0.14710	0.002217|0.002217	0.011976|0.011976	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.65|4.65	-1.12|-1.12	0.09808|0.09808	.|.	.|.	.|.	.|.	.|.	T|T	0.47322|0.47322	0.1439|0.1439	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47861|0.47861	-0.9084|-0.9084	4|4	.|.	.|.	.|.	.|.	9.8379|9.8379	0.40980|0.40980	0.0:0.4626:0.0:0.5374|0.0:0.4626:0.0:0.5374	.|.	.|.	.|.	.|.	C|M	475|1394	.|.	.|.	R|T	+|+	1|2	0|0	NBEAL2|NBEAL2	47021489|47021489	0.978000|0.978000	0.34361|0.34361	0.997000|0.997000	0.53966|0.53966	0.989000|0.989000	0.77384|0.77384	0.260000|0.260000	0.18424|0.18424	-0.088000|-0.088000	0.12506|0.12506	0.561000|0.561000	0.74099|0.74099	CGT|ACG	C|0.995;T|0.005	0.005	strong		0.662	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
FEM1A	55527	hgsc.bcm.edu	37	19	4793128	4793128	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4793128A>C	ENST00000269856.3	+	1	1401	c.1262A>C	c.(1261-1263)cAg>cCg	p.Q421P	AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	421					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GACATGCAACAGAGCAACCTG	0.602																																					p.Q421P		Atlas-SNP	.											.	FEM1A	41	.	0			c.A1262C						PASS	.						64.0	66.0	65.0					19																	4793128		2203	4299	6502	SO:0001583	missense	55527	exon1			TGCAACAGAGCAA	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"""Ankyrin repeat domain containing"""	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1262A>C	19.37:g.4793128A>C	ENSP00000269856:p.Gln421Pro	43.0	0.0	0		52.0	20.0	0.384615	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	37	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.547381	0.65311	.	.	ENSG00000141965	ENST00000269856	T	0.58652	0.32	5.07	5.07	0.68467	Tetratricopeptide-like helical (1);	0.000000	0.64402	U	0.000001	T	0.80481	0.4631	M	0.91406	3.205	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.84430	0.0576	10	0.52906	T	0.07	-21.7521	14.8247	0.70101	1.0:0.0:0.0:0.0	.	421	Q9BSK4	FEM1A_HUMAN	P	421	ENSP00000269856:Q421P	ENSP00000269856:Q421P	Q	+	2	0	FEM1A	4744128	1.000000	0.71417	0.993000	0.49108	0.698000	0.40448	9.119000	0.94362	1.906000	0.55180	0.402000	0.26972	CAG	.	.	none		0.602	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1		
PIEZO1	9780	hgsc.bcm.edu	37	16	88782777	88782777	+	Silent	SNP	G	G	A	rs34352064	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88782777G>A	ENST00000301015.9	-	48	7287	c.7041C>T	c.(7039-7041)gaC>gaT	p.D2347D	RP5-1142A6.9_ENST00000564984.1_RNA|MIR4722_ENST00000578292.1_RNA|PIEZO1_ENST00000327397.7_Silent_p.D215D	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2347					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						ACACAGACTGGTCCGAGGTGC	0.682													G|||	15	0.00299521	0.0	0.0072	5008	,	,		16535	0.0		0.0099	False		,,,				2504	0.0				p.D2347D		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C7041T						PASS	.						25.0	26.0	26.0					16																	88782777		692	1585	2277	SO:0001819	synonymous_variant	9780	exon48			AGACTGGTCCGAG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.7041C>T	16.37:g.88782777G>A		45.0	0.0	0		56.0	24.0	0.428571	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	7.859	0.725755	0.15439	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.54	2.48	0.30137	.	.	.	.	.	T	0.43743	0.1261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	-26.3943	4.5121	0.11917	0.0876:0.1553:0.5968:0.1604	rs34352064	.	.	.	S	2293	.	.	P	-	1	0	FAM38A	87310278	0.146000	0.22672	0.936000	0.37596	0.951000	0.60555	0.222000	0.17699	0.317000	0.23160	0.467000	0.42956	CCA	G|0.995;A|0.005	0.005	strong		0.682	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
UBAP2	55833	hgsc.bcm.edu	37	9	33998847	33998847	+	Missense_Mutation	SNP	T	T	C	rs149441020	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33998847T>C	ENST00000379238.1	-	3	232	c.115A>G	c.(115-117)Atg>Gtg	p.M39V	UBAP2_ENST00000539807.1_Start_Codon_SNP_p.M1V|UBAP2_ENST00000379239.4_5'UTR|UBAP2_ENST00000449054.1_Missense_Mutation_p.M39V|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000418786.2_Missense_Mutation_p.M39V|UBAP2_ENST00000360802.1_Missense_Mutation_p.M39V					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GCGAGACGCATCTGTTCAGCT	0.358													T|||	3	0.000599042	0.0	0.0	5008	,	,		19492	0.0		0.003	False		,,,				2504	0.0				p.M39V		Atlas-SNP	.											.	UBAP2	82	.	0			c.A115G						PASS	.	T	VAL/MET	0,4406		0,0,2203	104.0	99.0	101.0		115	6.2	1.0	9	dbSNP_134	101	2,8598	2.2+/-6.3	0,2,4298	yes	missense	UBAP2	NM_018449.2	21	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	39/1120	33998847	2,13004	2203	4300	6503	SO:0001583	missense	55833	exon3			GACGCATCTGTTC	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.115A>G	9.37:g.33998847T>C	ENSP00000368540:p.Met39Val	25.0	0.0	0		16.0	11.0	0.6875	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	19.13	3.767752	0.69878	0.0	2.33E-4	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000539807;ENST00000351580;ENST00000418786;ENST00000412543	T;T;T;T;T;T	0.27720	1.65;1.65;1.65;2.58;1.65;1.65	6.17	6.17	0.99709	UBA-like (1);	0.082223	0.85682	D	0.000000	T	0.32763	0.0840	L	0.40543	1.245	0.48696	D	0.999693	P;B;B;B;B;B	0.37731	0.607;0.291;0.225;0.053;0.192;0.125	B;B;B;B;B;B	0.40602	0.334;0.145;0.032;0.019;0.069;0.082	T	0.05053	-1.0909	10	0.54805	T	0.06	-8.1025	16.8222	0.85835	0.0:0.0:0.0:1.0	.	39;1;1;1;1;39	E7EWG4;F5H4D5;F5H2U4;F5H2C8;B4DH66;Q5T6F2	.;.;.;.;.;UBAP2_HUMAN	V	39;39;39;1;1;39;39;39	ENSP00000368540:M39V;ENSP00000416932:M39V;ENSP00000354039:M39V;ENSP00000439329:M1V;ENSP00000404436:M39V;ENSP00000414800:M39V	ENSP00000259602:M39V	M	-	1	0	UBAP2	33988847	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.845000	0.69437	2.371000	0.80710	0.533000	0.62120	ATG	T|0.999;C|0.001	0.001	strong		0.358	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
PCSK5	5125	hgsc.bcm.edu	37	9	78789900	78789900	+	Splice_Site	SNP	A	A	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78789900A>C	ENST00000545128.1	+	14	2294		c.e14-1		PCSK5_ENST00000376767.3_Splice_Site|PCSK5_ENST00000376752.4_Splice_Site	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TTATTTCTCAAGGTAAATTGA	0.413																																					.		Atlas-SNP	.											PCSK5_ENST00000545128,NS,carcinoma,0,3	PCSK5	329	3	0			c.1757-2A>C						PASS	.						118.0	114.0	116.0					9																	78789900		2203	4300	6503	SO:0001630	splice_region_variant	5125	exon14			TTCTCAAGGTAAA		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1757-1A>C	9.37:g.78789900A>C		164.0	0.0	0		153.0	10.0	0.0653595	NM_001190482	F5H2G7|Q13527|Q96EP4	Splice_Site	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.486799	0.84854	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0502	0.80755	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCSK5	77979720	1.000000	0.71417	0.931000	0.37212	0.991000	0.79684	8.652000	0.91083	2.197000	0.70478	0.528000	0.53228	.	.	.	none		0.413	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron
OR7G3	390883	hgsc.bcm.edu	37	19	9237554	9237554	+	Missense_Mutation	SNP	G	G	A	rs138008445	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9237554G>A	ENST00000305444.2	-	1	72	c.73C>T	c.(73-75)Ccc>Tcc	p.P25S		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AAGAGGATGGGCTGCAGCTCC	0.517													G|||	11	0.00219649	0.0038	0.0014	5008	,	,		18583	0.0		0.004	False		,,,				2504	0.001				p.P25S		Atlas-SNP	.											.	OR7G3	41	.	0			c.C73T						PASS	.	G	SER/PRO	18,4388	25.3+/-52.1	0,18,2185	83.0	79.0	80.0		73	1.8	0.4	19	dbSNP_134	80	45,8555	30.1+/-81.4	0,45,4255	yes	missense	OR7G3	NM_001001958.1	74	0,63,6440	AA,AG,GG		0.5233,0.4085,0.4844	benign	25/313	9237554	63,12943	2203	4300	6503	SO:0001583	missense	390883	exon1			GGATGGGCTGCAG		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.73C>T	19.37:g.9237554G>A	ENSP00000302867:p.Pro25Ser	113.0	0.0	0		132.0	62.0	0.469697	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.52	1.371909	0.24857	0.004085	0.005233	ENSG00000170920	ENST00000305444	T	0.00424	7.45	4.02	1.83	0.25207	.	0.925765	0.08843	N	0.885581	T	0.00300	0.0009	M	0.71581	2.175	0.22050	N	0.999397	P	0.45474	0.859	B	0.34242	0.178	T	0.49960	-0.8883	10	0.54805	T	0.06	.	7.5109	0.27573	0.0906:0.0:0.7443:0.1651	.	25	Q8NG95	OR7G3_HUMAN	S	25	ENSP00000302867:P25S	ENSP00000302867:P25S	P	-	1	0	OR7G3	9098554	0.000000	0.05858	0.355000	0.25773	0.017000	0.09413	-0.911000	0.04050	0.469000	0.27268	-0.259000	0.10710	CCC	G|0.995;A|0.005	0.005	strong		0.517	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
FOXO1	2308	hgsc.bcm.edu	37	13	41240299	41240299	+	Silent	SNP	C	C	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41240299C>A	ENST00000379561.5	-	1	435	c.51G>T	c.(49-51)ctG>ctT	p.L17L		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	17					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		GCGGCCGGGGCAGCGGCTCGA	0.741																																					p.L17L		Atlas-SNP	.											.	FOXO1	110	.	0			c.G51T						PASS	.						1.0	2.0	1.0					13																	41240299		1153	2574	3727	SO:0001819	synonymous_variant	2308	exon1			CCGGGGCAGCGGC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.51G>T	13.37:g.41240299C>A		3.0	0.0	0		11.0	5.0	0.454545	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	37	CCDS9371.1																																																																																			.	.	none		0.741	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
ALG14	199857	hgsc.bcm.edu	37	1	95538342	95538342	+	Missense_Mutation	SNP	C	C	A	rs139521179	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:95538342C>A	ENST00000370205.5	-	1	159	c.113G>T	c.(112-114)aGt>aTt	p.S38I	ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	38					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		TACCAAGATACTGAGAGACTC	0.582													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17973	0.0		0.004	False		,,,				2504	0.0				p.S38I		Atlas-SNP	.											.	ALG14	13	.	0			c.G113T						PASS	.	C	ILE/SER	3,4403	6.2+/-15.9	0,3,2200	128.0	116.0	121.0		113	5.0	1.0	1	dbSNP_134	121	40,8560	27.4+/-76.7	0,40,4260	yes	missense	ALG14	NM_144988.3	142	0,43,6460	AA,AC,CC		0.4651,0.0681,0.3306	benign	38/217	95538342	43,12963	2203	4300	6503	SO:0001583	missense	199857	exon1			AAGATACTGAGAG		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"""asparagine-linked glycosylation 14 homolog (yeast)"", ""asparagine-linked glycosylation 14 homolog (S. cerevisiae)"""			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.113G>T	1.37:g.95538342C>A	ENSP00000359224:p.Ser38Ile	58.0	0.0	0		61.0	29.0	0.47541	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	13.48	2.248804	0.39797	6.81E-4	0.004651	ENSG00000172339	ENST00000370205	T	0.46819	0.86	4.99	4.99	0.66335	.	0.528179	0.21965	N	0.066526	T	0.17959	0.0431	N	0.08118	0	0.38423	D	0.946221	P	0.36909	0.573	B	0.34824	0.19	T	0.15809	-1.0424	10	0.54805	T	0.06	-3.7389	15.8023	0.78463	0.0:1.0:0.0:0.0	.	38	Q96F25	ALG14_HUMAN	I	38	ENSP00000359224:S38I	ENSP00000359224:S38I	S	-	2	0	ALG14	95310930	0.853000	0.29707	0.993000	0.49108	0.346000	0.29079	1.131000	0.31406	2.591000	0.87537	0.591000	0.81541	AGT	C|0.997;A|0.003	0.003	strong		0.582	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988	
ME2	4200	hgsc.bcm.edu	37	18	48447462	48447462	+	Missense_Mutation	SNP	A	A	C	rs59409558	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:48447462A>C	ENST00000321341.5	+	10	1233	c.961A>C	c.(961-963)Aat>Cat	p.N321H	ME2_ENST00000382927.3_Missense_Mutation_p.N321H	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	321					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		TGGAATTGCAAATCTTATAGT	0.318													A|||	30	0.00599042	0.0	0.0058	5008	,	,		15027	0.003		0.0149	False		,,,				2504	0.0082				p.N321H		Atlas-SNP	.											.	ME2	49	.	0			c.A961C						PASS	.	A	HIS/ASN,HIS/ASN	20,4386	27.2+/-55.0	0,20,2183	53.0	55.0	54.0		961,961	5.9	1.0	18	dbSNP_129	54	99,8495	55.2+/-116.2	0,99,4198	yes	missense,missense	ME2	NM_001168335.1,NM_002396.4	68,68	0,119,6381	CC,CA,AA		1.152,0.4539,0.9154	benign,benign	321/480,321/585	48447462	119,12881	2203	4297	6500	SO:0001583	missense	4200	exon10			ATTGCAAATCTTA	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.961A>C	18.37:g.48447462A>C	ENSP00000321070:p.Asn321His	82.0	0.0	0		108.0	47.0	0.435185	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	2	0.0034965034965034965	10	0.013192612137203167	A	11.52	1.662037	0.29515	0.004539	0.01152	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.31769	1.48;1.48	5.92	5.92	0.95590	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.042144	0.85682	D	0.000000	T	0.23451	0.0567	L	0.52364	1.645	0.58432	D	0.999997	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.003	T	0.02805	-1.1108	10	0.32370	T	0.25	-20.0102	15.3462	0.74340	1.0:0.0:0.0:0.0	rs59409558	321;321	Q9BWL6;P23368	.;MAOM_HUMAN	H	321	ENSP00000321070:N321H;ENSP00000372384:N321H	ENSP00000321070:N321H	N	+	1	0	ME2	46701460	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.360000	0.59455	2.267000	0.75376	0.528000	0.53228	AAT	A|0.991;C|0.009	0.009	strong		0.318	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396	
COL24A1	255631	hgsc.bcm.edu	37	1	86591014	86591014	+	Silent	SNP	T	T	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86591014T>C	ENST00000370571.2	-	3	1371	c.1005A>G	c.(1003-1005)aaA>aaG	p.K335K	COL24A1_ENST00000436319.1_Silent_p.K335K	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	335					extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TGATCATTTCTTTGGCCTGAA	0.403																																					p.K335K		Atlas-SNP	.											.	COL24A1	202	.	0			c.A1005G						PASS	.						112.0	98.0	102.0					1																	86591014		1905	4128	6033	SO:0001819	synonymous_variant	255631	exon3			CATTTCTTTGGCC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1005A>G	1.37:g.86591014T>C		207.0	0.0	0		183.0	12.0	0.0655738	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																			.	.	none		0.403	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
HGSNAT	138050	hgsc.bcm.edu	37	8	43053062	43053062	+	Missense_Mutation	SNP	G	G	C	rs148632988	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:43053062G>C	ENST00000458501.2	+	17	1777	c.1777G>C	c.(1777-1779)Ggg>Cgg	p.G593R	HGSNAT_ENST00000521576.1_Missense_Mutation_p.G282R|HGSNAT_ENST00000379644.4_Missense_Mutation_p.G565R|HGSNAT_ENST00000297798.7_Missense_Mutation_p.G297R			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	593					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)			GGATGTGAAGGGGCTGTGGAC	0.557													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		17354	0.0		0.0089	False		,,,				2504	0.0092				p.G565R		Atlas-SNP	.											.	HGSNAT	85	.	0			c.G1693C						PASS	.	G	ARG/GLY	7,3871		0,7,1932	125.0	121.0	122.0		1693	5.1	1.0	8	dbSNP_134	122	87,8207		1,85,4061	yes	missense	HGSNAT	NM_152419.2	125	1,92,5993	CC,CG,GG		1.049,0.1805,0.7723	benign	565/636	43053062	94,12078	1939	4147	6086	SO:0001583	missense	138050	exon17			GTGAAGGGGCTGT		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.1777G>C	8.37:g.43053062G>C	ENSP00000389524:p.Gly593Arg	209.0	0.0	0		236.0	123.0	0.521186	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	37		11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	9.728	1.161382	0.21538	0.001805	0.01049	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	6.07	5.1	0.69264	.	0.372260	0.31438	N	0.007646	T	0.66015	0.2747	N	0.12443	0.215	0.45777	D	0.998663	B	0.12013	0.005	B	0.06405	0.002	T	0.64711	-0.6343	10	0.38643	T	0.18	-14.3505	5.7907	0.18359	0.2131:0.0:0.7869:0.0	.	593	Q68CP4	HGNAT_HUMAN	R	593;565;282;297	ENSP00000389524:G593R;ENSP00000368965:G565R;ENSP00000429029:G282R;ENSP00000297798:G297R	ENSP00000297798:G297R	G	+	1	0	HGSNAT	43172219	0.552000	0.26505	0.974000	0.42286	0.849000	0.48306	2.331000	0.43894	2.885000	0.99019	0.655000	0.94253	GGG	G|0.995;C|0.005	0.005	strong		0.557	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	
ARSI	340075	hgsc.bcm.edu	37	5	149677635	149677635	+	Silent	SNP	G	G	A	rs139203947	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149677635G>A	ENST00000328668.7	-	2	1431	c.852C>T	c.(850-852)taC>taT	p.Y284Y		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	284					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTAGAAACCGTAGCGCTTGA	0.602													G|||	5	0.000998403	0.0	0.0	5008	,	,		22146	0.0		0.005	False		,,,				2504	0.0				p.Y284Y		Atlas-SNP	.											.	ARSI	65	.	0			c.C852T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	39.0	33.0	35.0		852	-7.8	0.6	5	dbSNP_134	35	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	ARSI	NM_001012301.2		0,17,6486	AA,AG,GG		0.1744,0.0454,0.1307		284/570	149677635	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	340075	exon2			GAAACCGTAGCGC	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"""Arylsulfatase family"""	32521	protein-coding gene	gene with protein product		610009	"""arylsulfatase I"""			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.852C>T	5.37:g.149677635G>A		44.0	0.0	0		47.0	23.0	0.489362	NM_001012301	A1L3B0|B3KV22|B7XD03	Silent	SNP	ENST00000328668.7	37	CCDS34275.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301	
WASF3	10810	hgsc.bcm.edu	37	13	27250805	27250805	+	Missense_Mutation	SNP	G	G	T	rs139779405	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:27250805G>T	ENST00000335327.5	+	7	838	c.660G>T	c.(658-660)ttG>ttT	p.L220F	WASF3_ENST00000361042.4_Intron	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	220					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		ACAACAGGTTGTCTCAGAGTG	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		17714	0.0		0.002	False		,,,				2504	0.0				p.L220F		Atlas-SNP	.											.	WASF3	68	.	0			c.G660T						PASS	.	G	PHE/LEU	0,4406		0,0,2203	179.0	165.0	170.0		660	4.1	1.0	13	dbSNP_134	170	10,8590	7.7+/-29.5	0,10,4290	yes	missense	WASF3	NM_006646.5	22	0,10,6493	TT,TG,GG		0.1163,0.0,0.0769	possibly-damaging	220/503	27250805	10,12996	2203	4300	6503	SO:0001583	missense	10810	exon7			CAGGTTGTCTCAG	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.660G>T	13.37:g.27250805G>T	ENSP00000335055:p.Leu220Phe	72.0	0.0	0		69.0	34.0	0.492754	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.363	0.435000	0.12045	0.0	0.001163	ENSG00000132970	ENST00000335327	T	0.43688	0.94	5.77	4.05	0.47172	.	0.150888	0.49916	D	0.000139	T	0.32194	0.0821	L	0.36672	1.1	0.80722	D	1	B	0.20988	0.05	B	0.23716	0.048	T	0.06180	-1.0841	10	0.27082	T	0.32	-16.5533	10.5878	0.45292	0.2073:0.0:0.7927:0.0	.	220	Q9UPY6	WASF3_HUMAN	F	220	ENSP00000335055:L220F	ENSP00000335055:L220F	L	+	3	2	WASF3	26148805	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.331000	0.43894	0.798000	0.33994	0.591000	0.81541	TTG	A|0.000;G|0.999;T|0.001	0.001	strong		0.532	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1		
C12orf77	196415	hgsc.bcm.edu	37	12	25148824	25148824	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25148824G>T	ENST00000549828.1	-	3	528	c.324C>A	c.(322-324)aaC>aaA	p.N108K	C12orf77_ENST00000549262.1_Missense_Mutation_p.N53K|C12orf77_ENST00000434912.3_Missense_Mutation_p.N53K	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	108										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						TCTTTTCCGTGTTCATAAACG	0.463																																					p.N108K		Atlas-SNP	.											.	C12orf77	18	.	0			c.C324A						PASS	.						72.0	74.0	73.0					12																	25148824		1919	4117	6036	SO:0001583	missense	196415	exon3			TTCCGTGTTCATA	BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397			27282	protein-coding gene	gene with protein product						12477932	Standard	NM_001101339		Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.324C>A	12.37:g.25148824G>T	ENSP00000447146:p.Asn108Lys	178.0	0.0	0		209.0	58.0	0.277512	NM_001101339		Missense_Mutation	SNP	ENST00000549828.1	37	CCDS44846.1	.	.	.	.	.	.	.	.	.	.	G	8.521	0.868659	0.17322	.	.	ENSG00000226397	ENST00000549828;ENST00000549262;ENST00000434912	T;T;T	0.54071	0.64;0.59;0.59	2.79	1.84	0.25277	.	.	.	.	.	T	0.28764	0.0713	N	0.08118	0	0.09310	N	1	P	0.37101	0.582	B	0.33339	0.162	T	0.13872	-1.0493	9	0.87932	D	0	.	7.4561	0.27268	0.0:0.2699:0.7301:0.0	.	108	C9JDV5	CL097_HUMAN	K	108;53;53	ENSP00000447146:N108K;ENSP00000447028:N53K;ENSP00000403451:N53K	ENSP00000403451:N53K	N	-	3	2	C12orf77	25040091	0.000000	0.05858	0.008000	0.14137	0.002000	0.02628	-0.265000	0.08644	0.689000	0.31550	0.655000	0.94253	AAC	.	.	none		0.463	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339	
SGK1	6446	hgsc.bcm.edu	37	6	134495683	134495683	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495683G>C	ENST00000237305.7	-	2	206	c.118C>G	c.(118-120)Cag>Gag	p.Q40E	SGK1_ENST00000528577.1_Missense_Mutation_p.Q68E|SGK1_ENST00000413996.3_Missense_Mutation_p.Q54E|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.Q30E|SGK1_ENST00000475719.2_Missense_Mutation_p.Q40E|SGK1_ENST00000367858.5_Missense_Mutation_p.Q135E	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	40	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.Q40*(1)|p.Q135*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GCAATCTTCTGAATAAAGTCG	0.423											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q135E		Atlas-SNP	.											SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C403G						PASS	.						90.0	88.0	89.0					6																	134495683		2203	4300	6503	SO:0001583	missense	6446	exon4			TCTTCTGAATAAA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.118C>G	6.37:g.134495683G>C	ENSP00000237305:p.Gln40Glu	70.0	0.0	0	1611	46.0	16.0	0.347826	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.645700	0.87958	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.42513	1.47;1.47;1.47;1.47;1.47;1.47;0.97	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.48624	0.1510	M	0.73962	2.25	0.80722	D	1	P;P;P;P;D;P	0.54772	0.936;0.792;0.895;0.721;0.968;0.81	P;B;B;B;P;B	0.51170	0.511;0.337;0.41;0.373;0.661;0.23	T	0.39354	-0.9618	10	0.34782	T	0.22	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	68;54;40;30;135;40	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	E	135;54;40;30;68;40;104	ENSP00000356832:Q135E;ENSP00000396242:Q54E;ENSP00000237305:Q40E;ENSP00000356831:Q30E;ENSP00000434450:Q68E;ENSP00000434302:Q40E;ENSP00000435577:Q104E	ENSP00000237305:Q40E	Q	-	1	0	SGK1	134537376	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.783000	0.95769	0.655000	0.94253	CAG	.	.	none		0.423	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
CLCC1	23155	hgsc.bcm.edu	37	1	109477406	109477406	+	Silent	SNP	C	C	T	rs150029224	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109477406C>T	ENST00000369971.2	-	11	1671	c.1542G>A	c.(1540-1542)aaG>aaA	p.K514K	CLCC1_ENST00000369968.2_Silent_p.K329K|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369969.2_Silent_p.K393K|CLCC1_ENST00000356970.2_Silent_p.K514K|CLCC1_ENST00000302500.4_Silent_p.K393K|CLCC1_ENST00000415331.1_Silent_p.K464K|CLCC1_ENST00000348264.2_Silent_p.K329K|CLCC1_ENST00000369970.3_Silent_p.K464K|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Intron	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	514						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		TGAGCTGGGCCTTTTCCGCTG	0.592																																					p.K514K		Atlas-SNP	.											.	CLCC1	55	.	0			c.G1542A						PASS	.	C	,	0,4406		0,0,2203	145.0	130.0	135.0		1542,1392	5.9	0.2	1	dbSNP_134	135	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous,coding-synonymous	CLCC1	NM_001048210.1,NM_015127.3	,	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	,	514/552,464/502	109477406	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	23155	exon11			CTGGGCCTTTTCC	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"""Mid1-related chloride channel (yeast)"""					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1542G>A	1.37:g.109477406C>T		228.0	1.0	0.00438596		203.0	102.0	0.502463	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Silent	SNP	ENST00000369971.2	37	CCDS41362.1																																																																																			C|1.000;T|0.000	0.000	strong		0.592	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
LAMA4	3910	hgsc.bcm.edu	37	6	112493894	112493894	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:112493894T>A	ENST00000230538.7	-	12	1867	c.1470A>T	c.(1468-1470)gaA>gaT	p.E490D	LAMA4_ENST00000389463.4_Missense_Mutation_p.E483D|LAMA4_ENST00000522006.1_Missense_Mutation_p.E483D|LAMA4_ENST00000424408.2_Missense_Mutation_p.E483D	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	490	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GGTCAAGTGCTTCCTGGAGAT	0.567																																					p.E490D		Atlas-SNP	.											.	LAMA4	227	.	0			c.A1470T						PASS	.						112.0	92.0	99.0					6																	112493894		2203	4300	6503	SO:0001583	missense	3910	exon12			AAGTGCTTCCTGG		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.1470A>T	6.37:g.112493894T>A	ENSP00000230538:p.Glu490Asp	109.0	0.0	0		100.0	41.0	0.41	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	T	5.231	0.228154	0.09916	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.51	-2.99	0.05497	Laminin I (1);	0.481995	0.24449	N	0.038440	T	0.06096	0.0158	L	0.50333	1.59	0.80722	D	1	P;P	0.51057	0.941;0.928	P;P	0.51516	0.672;0.597	T	0.24012	-1.0172	10	0.16420	T	0.52	.	12.0218	0.53348	0.0:0.6685:0.0:0.3315	.	490;483	Q16363;Q16363-2	LAMA4_HUMAN;.	D	490;483;483;483	ENSP00000230538:E490D;ENSP00000429488:E483D;ENSP00000374114:E483D;ENSP00000416470:E483D	ENSP00000230538:E490D	E	-	3	2	LAMA4	112600587	0.999000	0.42202	0.971000	0.41717	0.337000	0.28794	0.376000	0.20535	-0.328000	0.08539	-0.371000	0.07208	GAA	.	.	none		0.567	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
MBOAT7	79143	hgsc.bcm.edu	37	19	54687453	54687453	+	Silent	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54687453G>A	ENST00000245615.1	-	5	924	c.444C>T	c.(442-444)tcC>tcT	p.S148S	MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000431666.2_Silent_p.S75S|MBOAT7_ENST00000391754.1_Silent_p.S148S|MBOAT7_ENST00000338624.6_Silent_p.S75S	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	148					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCTCCATCAGGGAGGGCACGT	0.612																																					p.S148S	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.C444T						PASS	.						121.0	93.0	102.0					19																	54687453		2203	4300	6503	SO:0001819	synonymous_variant	79143	exon5			CATCAGGGAGGGC	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"""lysophosphatidylinositol acyltransferase"""	606048	"""leukocyte receptor cluster (LRC) member 4"""	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.444C>T	19.37:g.54687453G>A		121.0	0.0	0		121.0	40.0	0.330579	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Silent	SNP	ENST00000245615.1	37	CCDS12883.1																																																																																			.	.	none		0.612	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298	
GRM6	2916	hgsc.bcm.edu	37	5	178415983	178415983	+	Missense_Mutation	SNP	G	G	A	rs5019554	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178415983G>A	ENST00000517717.1	-	7	1345	c.1307C>T	c.(1306-1308)aCt>aTt	p.T436I	GRM6_ENST00000231188.5_Missense_Mutation_p.T436I|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	436					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CCGCCCATCAGTGGGTTCCAT	0.627													G|||	13	0.00259585	0.0	0.0086	5008	,	,		12866	0.0		0.007	False		,,,				2504	0.0				p.T436I		Atlas-SNP	.											.	GRM6	149	.	0			c.C1307T						PASS	.						72.0	69.0	70.0					5																	178415983		2203	4300	6503	SO:0001583	missense	2916	exon6			CCATCAGTGGGTT	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1307C>T	5.37:g.178415983G>A	ENSP00000430767:p.Thr436Ile	163.0	0.0	0		122.0	49.0	0.401639	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	0.962	-0.702814	0.03255	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.86562	-2.14;-2.14	5.28	5.28	0.74379	Extracellular ligand-binding receptor (1);	.	.	.	.	T	0.56963	0.2021	N	0.01197	-0.965	0.34940	D	0.750266	B;B	0.31383	0.321;0.001	B;B	0.32724	0.151;0.006	T	0.68277	-0.5451	9	0.06757	T	0.87	.	10.2758	0.43510	0.09:0.0:0.91:0.0	rs5019554;rs5019555;rs17839800	476;436	E7EX65;O15303	.;GRM6_HUMAN	I	476;436;436	ENSP00000231188:T436I;ENSP00000430767:T436I	ENSP00000231188:T436I	T	-	2	0	GRM6	178348589	0.983000	0.35010	0.958000	0.39756	0.161000	0.22273	6.201000	0.72124	2.643000	0.89663	0.555000	0.69702	ACT	A|0.008;G|0.992	0.008	strong		0.627	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
SYNGAP1	8831	hgsc.bcm.edu	37	6	33409006	33409006	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33409006G>A	ENST00000418600.2	+	12	2071	c.1970G>A	c.(1969-1971)tGg>tAg	p.W657*	SYNGAP1_ENST00000293748.5_Nonsense_Mutation_p.W657*|SYNGAP1_ENST00000428982.2_Nonsense_Mutation_p.W598*|SYNGAP1_ENST00000496374.1_3'UTR|MIR5004_ENST00000579078.1_RNA	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	657					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GAGCTGGAATGGGGTTCCATG	0.478																																					p.W657X		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.G1970A						PASS	.						152.0	131.0	138.0					6																	33409006		2203	4300	6503	SO:0001587	stop_gained	8831	exon12			TGGAATGGGGTTC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1970G>A	6.37:g.33409006G>A	ENSP00000403636:p.Trp657*	70.0	0.0	0		118.0	11.0	0.0932203	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Nonsense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	39	7.288432	0.98189	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7055	0.45952	0.0:0.0:0.8099:0.1901	.	.	.	.	X	657;657;657;598	.	ENSP00000293748:W657X	W	+	2	0	SYNGAP1	33516984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.669000	0.83911	2.573000	0.86826	0.655000	0.94253	TGG	.	.	none		0.478	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
TMEM135	65084	hgsc.bcm.edu	37	11	87020670	87020670	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:87020670T>G	ENST00000305494.5	+	10	931	c.892T>G	c.(892-894)Ttc>Gtc	p.F298V	TMEM135_ENST00000340353.7_Missense_Mutation_p.F276V|TMEM135_ENST00000535167.1_Missense_Mutation_p.F159V|TMEM135_ENST00000532959.1_Missense_Mutation_p.F169V	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	298					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TAAAGAAAACTTCCAGCTTGG	0.393																																					p.F298V		Atlas-SNP	.											.	TMEM135	40	.	0			c.T892G						PASS	.						85.0	93.0	90.0					11																	87020670		2201	4299	6500	SO:0001583	missense	65084	exon10			GAAAACTTCCAGC	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.892T>G	11.37:g.87020670T>G	ENSP00000306344:p.Phe298Val	65.0	0.0	0		70.0	20.0	0.285714	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Missense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.792969	0.90453	.	.	ENSG00000166575	ENST00000340353;ENST00000544294;ENST00000532959;ENST00000305494;ENST00000535167	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.45357	0.1338	L	0.46741	1.465	0.80722	D	1	P;D	0.62365	0.48;0.991	B;P	0.62184	0.143;0.899	T	0.24621	-1.0155	9	.	.	.	-29.3596	14.8495	0.70286	0.0:0.0:0.0:1.0	.	276;298	Q86UB9-2;Q86UB9	.;TM135_HUMAN	V	276;135;169;298;159	ENSP00000345513:F276V;ENSP00000436179:F169V;ENSP00000306344:F298V;ENSP00000439525:F159V	.	F	+	1	0	TMEM135	86698318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.915000	0.87484	2.160000	0.67779	0.482000	0.46254	TTC	.	.	none		0.393	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	
WDR49	151790	hgsc.bcm.edu	37	3	167240215	167240215	+	Missense_Mutation	SNP	C	C	T	rs202225646		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167240215C>T	ENST00000308378.3	-	12	1911	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	WDR49_ENST00000453925.2_Intron|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.V361M	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	536										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TCACTTTCCACTAAATTAGTA	0.294																																					p.V536M		Atlas-SNP	.											.	WDR49	188	.	0			c.G1606A						PASS	.	C	MET/VAL	0,4406		0,0,2203	66.0	70.0	68.0		1606	-1.5	0.0	3		68	2,8596	2.2+/-6.3	0,2,4297	yes	missense	WDR49	NM_178824.3	21	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign	536/698	167240215	2,13002	2203	4299	6502	SO:0001583	missense	151790	exon12			TTTCCACTAAATT	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1606G>A	3.37:g.167240215C>T	ENSP00000311343:p.Val536Met	47.0	0.0	0		72.0	39.0	0.541667	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	C	2.789	-0.251853	0.05829	0.0	2.33E-4	ENSG00000174776	ENST00000308378;ENST00000476376	T;T	0.53423	0.62;1.92	5.23	-1.55	0.08558	WD40 repeat-like-containing domain (1);	0.994051	0.08174	N	0.986607	T	0.24236	0.0587	N	0.04203	-0.255	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.20773	-1.0265	10	0.37606	T	0.19	.	9.614	0.39681	0.0:0.4515:0.0:0.5485	.	536	Q8IV35	WDR49_HUMAN	M	536;361	ENSP00000311343:V536M;ENSP00000420508:V361M	ENSP00000311343:V536M	V	-	1	0	WDR49	168722909	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.104000	0.15313	-0.173000	0.10761	-0.312000	0.09012	GTG	.	.	weak		0.294	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
SASH1	23328	hgsc.bcm.edu	37	6	148840980	148840980	+	Missense_Mutation	SNP	C	C	T	rs116958992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:148840980C>T	ENST00000367467.3	+	10	1635	c.1160C>T	c.(1159-1161)tCc>tTc	p.S387F		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	387					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GTGTCCCGCTCCCTCACCGAG	0.567													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		17240	0.001		0.0089	False		,,,				2504	0.0031				p.S387F		Atlas-SNP	.											.	SASH1	123	.	0			c.C1160T						PASS	.	C	PHE/SER	6,4398		0,6,2196	17.0	19.0	18.0		1160	4.7	1.0	6	dbSNP_132	18	86,8512		1,84,4214	yes	missense	SASH1	NM_015278.3	155	1,90,6410	TT,TC,CC		1.0002,0.1362,0.7076	probably-damaging	387/1248	148840980	92,12910	2202	4299	6501	SO:0001583	missense	23328	exon10			CCCGCTCCCTCAC	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1160C>T	6.37:g.148840980C>T	ENSP00000356437:p.Ser387Phe	21.0	0.0	0		16.0	6.0	0.375	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	21.4	4.136970	0.77775	0.001362	0.010002	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.49720	0.77	5.6	4.74	0.60224	.	0.048773	0.85682	N	0.000000	T	0.25044	0.0608	L	0.34521	1.04	0.53005	D	0.99996	P;P	0.47106	0.89;0.89	B;B	0.39840	0.311;0.197	T	0.12400	-1.0549	10	0.72032	D	0.01	-22.8395	14.3413	0.66627	0.0:0.929:0.0:0.071	.	368;387	Q6P4R9;O94885	.;SASH1_HUMAN	F	387;148	ENSP00000356437:S387F	ENSP00000356437:S387F	S	+	2	0	SASH1	148882673	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.247000	0.78257	1.380000	0.46344	0.650000	0.86243	TCC	C|0.994;T|0.006	0.006	strong		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
WNT7B	7477	hgsc.bcm.edu	37	22	46319203	46319203	+	Missense_Mutation	SNP	G	G	A	rs147287645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46319203G>A	ENST00000339464.4	-	4	957	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	WNT7B_ENST00000409496.3_Missense_Mutation_p.R199W|WNT7B_ENST00000410089.1_Missense_Mutation_p.R179W	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	195					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		AGCTGCATCCGGTCCTCTAGA	0.657																																					p.R195W		Atlas-SNP	.											.	WNT7B	45	.	0			c.C583T						PASS	.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	35.0	32.0	33.0		583	2.2	1.0	22	dbSNP_134	33	0,8598		0,0,4299	no	missense	WNT7B	NM_058238.2	101	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	195/350	46319203	1,13003	2203	4299	6502	SO:0001583	missense	7477	exon4			GCATCCGGTCCTC	AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.583C>T	22.37:g.46319203G>A	ENSP00000341032:p.Arg195Trp	63.0	0.0	0		66.0	18.0	0.272727	NM_058238	B8A596|Q96Q12	Missense_Mutation	SNP	ENST00000339464.4	37	CCDS33667.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.685148	0.29872	2.27E-4	0.0	ENSG00000188064	ENST00000339464;ENST00000410089;ENST00000409496	T;T;T	0.76578	-1.03;-1.03;-1.03	3.33	2.19	0.27852	.	0.060599	0.64402	U	0.000011	T	0.79639	0.4480	L	0.58810	1.83	0.80722	D	1	P;D	0.63046	0.939;0.992	P;P	0.56916	0.809;0.809	T	0.77787	-0.2457	10	0.38643	T	0.18	.	9.4282	0.38592	0.0:0.0:0.6255:0.3745	.	199;195	A8K0G1;P56706	.;WNT7B_HUMAN	W	195;179;199	ENSP00000341032:R195W;ENSP00000386781:R179W;ENSP00000386546:R199W	ENSP00000341032:R195W	R	-	1	2	WNT7B	44697867	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	2.986000	0.49370	1.579000	0.49836	0.305000	0.20034	CGG	G|1.000;A|0.000	0.000	weak		0.657	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238	
BAZ1B	9031	hgsc.bcm.edu	37	7	72883898	72883898	+	Missense_Mutation	SNP	G	G	A	rs145043036	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:72883898G>A	ENST00000339594.4	-	9	3153	c.2815C>T	c.(2815-2817)Cat>Tat	p.H939Y	BAZ1B_ENST00000404251.1_Missense_Mutation_p.H939Y	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	939					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTGCAGTGATGGTTGAATCGG	0.433													G|||	5	0.000998403	0.0	0.0029	5008	,	,		21118	0.0		0.003	False		,,,				2504	0.0				p.H939Y	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.C2815T						PASS	.	G	TYR/HIS	2,4404	6.2+/-15.9	0,2,2201	238.0	193.0	208.0		2815	3.8	0.8	7	dbSNP_134	208	10,8590	7.7+/-29.5	0,10,4290	yes	missense	BAZ1B	NM_032408.3	83	0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923	benign	939/1484	72883898	12,12994	2203	4300	6503	SO:0001583	missense	9031	exon9			AGTGATGGTTGAA	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2815C>T	7.37:g.72883898G>A	ENSP00000342434:p.His939Tyr	136.0	0.0	0		117.0	59.0	0.504274	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	3.549	-0.092107	0.07053	4.54E-4	0.001163	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.58060	0.36;0.36	5.59	3.78	0.43462	.	0.277384	0.41001	D	0.000975	T	0.23133	0.0559	N	0.08118	0	0.32807	D	0.500921	B	0.24483	0.104	B	0.19946	0.027	T	0.25047	-1.0143	10	0.27785	T	0.31	-8.3342	11.8585	0.52453	0.1431:0.0:0.8569:0.0	.	939	Q9UIG0	BAZ1B_HUMAN	Y	939	ENSP00000342434:H939Y;ENSP00000385442:H939Y	ENSP00000342434:H939Y	H	-	1	0	BAZ1B	72521834	1.000000	0.71417	0.761000	0.31378	0.591000	0.36615	4.342000	0.59341	0.722000	0.32252	-0.137000	0.14449	CAT	G|0.999;A|0.001	0.001	strong		0.433	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
IZUMO1	284359	hgsc.bcm.edu	37	19	49245518	49245518	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49245518T>G	ENST00000332955.2	-	7	1095	c.548A>C	c.(547-549)gAg>gCg	p.E183A	RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	183	Ig-like C2-type.				cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CCAGTTTAACTCACAGTCCAG	0.478																																					p.E183A		Atlas-SNP	.											.	IZUMO1	30	.	0			c.A548C						PASS	.						186.0	168.0	174.0					19																	49245518		2203	4300	6503	SO:0001583	missense	284359	exon7			TTTAACTCACAGT	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.548A>C	19.37:g.49245518T>G	ENSP00000327786:p.Glu183Ala	134.0	0.0	0		129.0	31.0	0.24031	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287181	0.40494	.	.	ENSG00000182264	ENST00000332955	D	0.83992	-1.79	4.57	2.39	0.29439	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.196760	0.05963	N	0.641060	T	0.73063	0.3539	L	0.29908	0.895	0.09310	N	1	P	0.42518	0.782	B	0.37888	0.26	T	0.59392	-0.7463	10	0.31617	T	0.26	-14.0882	7.3146	0.26493	0.3508:0.0:0.0:0.6491	.	183	Q8IYV9	IZUM1_HUMAN	A	183	ENSP00000327786:E183A	ENSP00000327786:E183A	E	-	2	0	IZUMO1	53937330	0.076000	0.21285	0.015000	0.15790	0.791000	0.44710	0.781000	0.26774	0.316000	0.23135	0.459000	0.35465	GAG	.	.	none		0.478	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
